1
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Medvedev P. Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond. COMMUNICATIONS OF THE ACM 2023; 66:118-125. [PMID: 38736702 PMCID: PMC11087067 DOI: 10.1145/3571723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
A case study reveals the theoretical analysis of algorithms is not always as helpful as standard dogma might suggest.
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Affiliation(s)
- Paul Medvedev
- Department of Computer Science and Engineering and the Department of Biochemistry and Molecular Biology and the Director of the Center for Computational Biology and Bioinformatics at Pennsylvania State University, University Park, PA, USA
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2
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Rahman A, Pachter L. SWALO: scaffolding with assembly likelihood optimization. Nucleic Acids Res 2021; 49:e117. [PMID: 34417615 PMCID: PMC8599790 DOI: 10.1093/nar/gkab717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/16/2021] [Accepted: 08/16/2021] [Indexed: 01/01/2023] Open
Abstract
Scaffolding, i.e. ordering and orienting contigs is an important step in genome assembly. We present a method for scaffolding using second generation sequencing reads based on likelihoods of genome assemblies. A generative model for sequencing is used to obtain maximum likelihood estimates of gaps between contigs and to estimate whether linking contigs into scaffolds would lead to an increase in the likelihood of the assembly. We then link contigs if they can be unambiguously joined or if the corresponding increase in likelihood is substantially greater than that of other possible joins of those contigs. The method is implemented in a tool called Swalo with approximations to make it efficient and applicable to large datasets. Analysis on real and simulated datasets reveals that it consistently makes more or similar number of correct joins as other scaffolders while linking very few contigs incorrectly, thus outperforming other scaffolders and demonstrating that substantial improvement in genome assembly may be achieved through the use of statistical models. Swalo is freely available for download at https://atifrahman.github.io/SWALO/.
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Affiliation(s)
- Atif Rahman
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA.,Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh
| | - Lior Pachter
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA.,Departments of Mathematics and Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA.,Departments of Biology and Computing & Mathematical Sciences, California Institute of Technology, Pasadena, CA 91103, USA
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3
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Ayling M, Clark MD, Leggett RM. New approaches for metagenome assembly with short reads. Brief Bioinform 2021; 21:584-594. [PMID: 30815668 PMCID: PMC7299287 DOI: 10.1093/bib/bbz020] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023] Open
Abstract
In recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.
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Affiliation(s)
- Martin Ayling
- Earlham Institute, Norwich Research Park, Norwich, UK
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4
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Břinda K, Baym M, Kucherov G. Simplitigs as an efficient and scalable representation of de Bruijn graphs. Genome Biol 2021; 22:96. [PMID: 33823902 PMCID: PMC8025321 DOI: 10.1186/s13059-021-02297-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/10/2021] [Indexed: 12/30/2022] Open
Abstract
de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and demonstrate that simplitigs provide a substantial improvement in the cumulative sequence length and their number. When combined with the commonly used Burrows-Wheeler Transform index, simplitigs reduce memory, and index loading and query times, as demonstrated with large-scale examples of GenBank bacterial pan-genomes.
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Affiliation(s)
- Karel Břinda
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA and Broad Institute of MIT and Harvard, Cambridge, USA.
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA.
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA and Broad Institute of MIT and Harvard, Cambridge, USA
| | - Gregory Kucherov
- CNRS/LIGM Univ Gustave Eiffel, Marne-la-Vallée, France
- Skolkovo Institute of Science and Technology, Moscow, Russia
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5
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Steyaert A, Audenaert P, Fostier J. Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields. BMC Bioinformatics 2020; 21:402. [PMID: 32928110 PMCID: PMC7491180 DOI: 10.1186/s12859-020-03740-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/04/2020] [Indexed: 12/01/2022] Open
Abstract
Background De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence difficult. A key step in this process is the inference of the multiplicities of nodes and arcs in the graph. These multiplicities correspond to the number of times each k-mer (resp. k+1-mer) implied by a node (resp. arc) is present in the genomic sequence. Determining multiplicities thus reveals the repeat structure and presence of sequencing errors. Multiplicities of nodes/arcs in the de Bruijn graph are reflected in their coverage, however, coverage variability and coverage biases render their determination ambiguous. Current methods to determine node/arc multiplicities base their decisions solely on the information in nodes and arcs individually, under-utilising the information present in the sequencing data. Results To improve the accuracy with which node and arc multiplicities in a de Bruijn graph are inferred, we developed a conditional random field (CRF) model to efficiently combine the coverage information within each node/arc individually with the information of surrounding nodes and arcs. Multiplicities are thus collectively assigned in a more consistent manner. Conclusions We demonstrate that the CRF model yields significant improvements in accuracy and a more robust expectation-maximisation parameter estimation. True k-mers can be distinguished from erroneous k-mers with a higher F1 score than existing methods. A C++11 implementation is available at https://github.com/biointec/detoxunder the GNU AGPL v3.0 license.
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6
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Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 2020; 587:246-251. [PMID: 33177663 PMCID: PMC7673649 DOI: 10.1038/s41586-020-2871-y] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1-3. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database4 increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies5 are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus6, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.
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Affiliation(s)
- Joel Armstrong
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Adam M Novak
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Alden Deran
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Duo Xie
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Diane Genereux
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Jeremy Johnson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Voichita Dana Marinescu
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jessica Alföldi
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Robert S Harris
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - David Haussler
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Elinor Karlsson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Erich D Jarvis
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA.
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7
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Rautiainen M, Marschall T. GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol 2020; 21:253. [PMID: 32972461 PMCID: PMC7513500 DOI: 10.1186/s13059-020-02157-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 08/26/2020] [Indexed: 02/07/2023] Open
Abstract
Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph. Yet, so far, this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory. When employing GraphAligner for error correction, we find it to be more than twice as accurate and over 12x faster than extant tools.Availability: Package manager: https://anaconda.org/bioconda/graphaligner and source code: https://github.com/maickrau/GraphAligner.
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Affiliation(s)
- Mikko Rautiainen
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, 66123, Germany.
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, 66123, Germany.
- Saarbrücken Graduate School for Computer Science, Saarland Informatics Campus E1.3, Saarbrücken, 66123, Germany.
| | - Tobias Marschall
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 5, Düsseldorf, 40225, Germany.
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8
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Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino DR. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics 2020; 35:5318-5320. [PMID: 31368484 PMCID: PMC6954646 DOI: 10.1093/bioinformatics/btz597] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/27/2019] [Accepted: 07/26/2019] [Indexed: 12/19/2022] Open
Abstract
Motivation Compared to traditional haploid reference genomes, graph genomes are an efficient and compact data structure for storing multiple genomic sequences, for storing polymorphisms or for mapping sequencing reads with greater sensitivity. Further, graphs are well-studied computer science objects that can be efficiently analyzed. However, their adoption in genomic research is slow, in part because of the cognitive difficulty in interpreting graphs. Results We present an intuitive graphical representation for graph genomes that re-uses well-honed techniques developed to display public transport networks, and demonstrate it as a web tool. Availability and implementation Code:https://github.com/vgteam/sequenceTubeMap. Demonstration https://vgteam.github.io/sequenceTubeMap/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wolfgang Beyer
- UC Santa Cruz Genomics Institute.,Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Adam M Novak
- UC Santa Cruz Genomics Institute.,Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute.,Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Jeffrey Chan
- UC Santa Cruz Genomics Institute.,Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Vanessa Tan
- UC Santa Cruz Genomics Institute.,Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute.,Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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9
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Yanes L, Garcia Accinelli G, Wright J, Ward BJ, Clavijo BJ. A Sequence Distance Graph framework for genome assembly and analysis. F1000Res 2019; 8:1490. [PMID: 31723420 PMCID: PMC6833988 DOI: 10.12688/f1000research.20233.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2019] [Indexed: 11/20/2022] Open
Abstract
The Sequence Distance Graph (SDG) framework works with genome assembly graphs and raw data from paired, linked and long reads. It includes a simple deBruijn graph module, and can import graphs using the graphical fragment assembly (GFA) format. It also maps raw reads onto graphs, and provides a Python application programming interface (API) to navigate the graph, access the mapped and raw data and perform interactive or scripted analyses. Its complete workspace can be dumped to and loaded from disk, decoupling mapping from analysis and supporting multi-stage pipelines. We present the design and implementation of the framework, and example analyses scaffolding a short read graph with long reads, and navigating paths in a heterozygous graph for a simulated parent-offspring trio dataset. SDG is freely available under the MIT license at https://github.com/bioinfologics/sdg.
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Affiliation(s)
- Luis Yanes
- Earlham Institute, Norwich, Norfolk, NR4 7UZ, UK
| | | | | | - Ben J. Ward
- Earlham Institute, Norwich, Norfolk, NR4 7UZ, UK
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10
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Salmela L, Tomescu AI. Safely Filling Gaps with Partial Solutions Common to All Solutions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:617-626. [PMID: 29994355 DOI: 10.1109/tcbb.2017.2785831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Gap filling has emerged as a natural sub-problem of many de novo genome assembly projects. The gap filling problem generally asks for an $s$s-$t$t path in an assembly graph whose length matches the gap length estimate. Several methods have addressed it, but only few have focused on strategies for dealing with multiple gap filling solutions and for guaranteeing reliable results. Such strategies include reporting only unique solutions, or exhaustively enumerating all filling solutions and heuristically creating their consensus. Our main contribution is a new method for reliable gap filling: filling gaps with those sub-paths common to all gap filling solutions. We call these partial solutions safe, following the framework of (Tomescu and Medvedev, RECOMB 2016). We give an efficient safe algorithm running in $O(dm)$O(dm) time and space, where $d$d is the gap length estimate and $m$m is the number of edges of the assembly graph. To show the benefits of this method, we implemented this algorithm for the problem of filling gaps in scaffolds. Our experimental results on bacterial and on conservative human assemblies show that, on average, our method can retrieve over 73 percent more safe and correct bases as compared to previous methods, with a similar precision.
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11
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Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D. A Flow Procedure for Linearization of Genome Sequence Graphs. J Comput Biol 2018; 25:664-676. [PMID: 29792514 PMCID: PMC6067104 DOI: 10.1089/cmb.2017.0248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within a species, a genome sequence graph. A sequence graph represents a set of individual haploid reference genomes as paths in a single graph. When that set of reference genomes is sufficiently diverse, the sequence graph implicitly contains all frequent human genetic variations, including translocations, inversions, deletions, and insertions. In representing a set of genomes as a sequence graph, one encounters certain challenges. One of the most important is the problem of graph linearization, essential both for efficiency of storage and access, and for natural graph visualization and compatibility with other tools. The goal of graph linearization is to order nodes of the graph in such a way that operations such as access, traversal, and visualization are as efficient and effective as possible. A new algorithm for the linearization of sequence graphs, called the flow procedure (FP), is proposed in this article. Comparative experimental evaluation of the FP against other algorithms shows that it outperforms its rivals in the metrics most relevant to sequence graphs.
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Affiliation(s)
- David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California
| | - Maciej Smuga-Otto
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California
| | - Jordan M. Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California
| | - Adam M. Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California
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12
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Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G. Superbubbles, Ultrabubbles, and Cacti. J Comput Biol 2018; 25:649-663. [PMID: 29461862 DOI: 10.1089/cmb.2017.0251] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genetics, the possible paths through a superbubble can be considered to represent the set of possible sequences at a location in a genome. Bidirected and biedged graphs are a generalization of digraphs that are increasingly being used to more fully represent genome assembly and variation problems. In this study, we define snarls and ultrabubbles, generalizations of superbubbles for bidirected and biedged graphs, and give an efficient algorithm for the detection of these more general structures. Key to this algorithm is the cactus graph, which, we show, encodes the nested decomposition of a graph into snarls and ultrabubbles within its structure. We propose and demonstrate empirically that this decomposition on bidirected and biedged graphs solves a fundamental problem by defining genetic sites for any collection of genomic variations, including complex structural variations, without need for any single reference genome coordinate system. Further, the nesting of the decomposition gives a natural way to describe and model variations contained within large variations, a case not currently dealt with by existing formats [e.g., variant cell format (VCF)].
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Affiliation(s)
- Benedict Paten
- 1 UC Santa Cruz Genomics Institute, University of California Santa Cruz , Santa Cruz, California
| | - Jordan M Eizenga
- 1 UC Santa Cruz Genomics Institute, University of California Santa Cruz , Santa Cruz, California
| | - Yohei M Rosen
- 1 UC Santa Cruz Genomics Institute, University of California Santa Cruz , Santa Cruz, California
| | - Adam M Novak
- 1 UC Santa Cruz Genomics Institute, University of California Santa Cruz , Santa Cruz, California
| | - Erik Garrison
- 2 Wellcome Trust Sanger Institute , Cambridge, United Kingdom
| | - Glenn Hickey
- 1 UC Santa Cruz Genomics Institute, University of California Santa Cruz , Santa Cruz, California
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13
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Obscura Acosta N, Mäkinen V, Tomescu AI. A safe and complete algorithm for metagenomic assembly. Algorithms Mol Biol 2018; 13:3. [PMID: 29445416 PMCID: PMC5802251 DOI: 10.1186/s13015-018-0122-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 01/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bacterial species present in a sequencing sample. This problem can be naturally formulated as finding a collection of circular walks of a directed graph G that together cover all nodes, or edges, of G. Approach We address this problem with the “safe and complete” framework of Tomescu and Medvedev (Research in computational Molecular biology—20th annual conference, RECOMB 9649:152–163, 2016). An algorithm is called safe if it returns only those walks (also called safe) that appear as subwalk in all metagenomic assembly solutions for G. A safe algorithm is called complete if it returns all safe walks of G. Results We give graph-theoretic characterizations of the safe walks of G, and a safe and complete algorithm finding all safe walks of G. In the node-covering case, our algorithm runs in time \documentclass[12pt]{minimal}
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\begin{document}$$O(m^2 + n^3)$$\end{document}O(m2+n3), and in the edge-covering case it runs in time \documentclass[12pt]{minimal}
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\begin{document}$$O(m^2n)$$\end{document}O(m2n); n and m denote the number of nodes and edges, respectively, of G. This algorithm constitutes the first theoretical tight upper bound on what can be safely assembled from metagenomic reads using this problem formulation.
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14
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Shomorony I, Kim SH, Courtade TA, Tse DNC. Information-optimal genome assembly via sparse read-overlap graphs. Bioinformatics 2017; 32:i494-i502. [PMID: 27587667 DOI: 10.1093/bioinformatics/btw450] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence? RESULTS Based on insights from this information feasibility question, we present an algorithm-the Not-So-Greedy algorithm-to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50. AVAILABILITY Available at github.com/samhykim/nsg CONTACT courtade@eecs.berkeley.edu or dntse@stanford.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ilan Shomorony
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, USA
| | - Samuel H Kim
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, USA
| | - Thomas A Courtade
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, USA
| | - David N C Tse
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, USA Department of Electrical Engineering, Stanford University, Stanford, CA, USA
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15
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Novak AM, Garrison E, Paten B. A graph extension of the positional Burrows-Wheeler transform and its applications. Algorithms Mol Biol 2017; 12:18. [PMID: 28702075 PMCID: PMC5505026 DOI: 10.1186/s13015-017-0109-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/17/2017] [Indexed: 01/23/2023] Open
Abstract
We present a generalization of the positional Burrows-Wheeler transform, or PBWT, to genome graphs, which we call the gPBWT. A genome graph is a collapsed representation of a set of genomes described as a graph. In a genome graph, a haplotype corresponds to a restricted form of walk. The gPBWT is a compressible representation of a set of these graph-encoded haplotypes that allows for efficient subhaplotype match queries. We give efficient algorithms for gPBWT construction and query operations. As a demonstration, we use the gPBWT to quickly count the number of haplotypes consistent with random walks in a genome graph, and with the paths taken by mapped reads; results suggest that haplotype consistency information can be practically incorporated into graph-based read mappers. We estimate that with the gPBWT of the order of 100,000 diploid genomes, including all forms structural variation, could be stored and made searchable for haplotype queries using a single large compute node.
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Affiliation(s)
- Adam M. Novak
- Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA 95064 USA
| | - Erik Garrison
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA 95064 USA
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16
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Abstract
The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph-based models. Here, we survey various projects underway to build and apply these graph-based structures-which we collectively refer to as genome graphs-and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce.
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Affiliation(s)
- Benedict Paten
- Genomics Institute, CBSE, 501C Engineering 2, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Adam M Novak
- Genomics Institute, CBSE, 501C Engineering 2, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Jordan M Eizenga
- Genomics Institute, CBSE, 501C Engineering 2, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Erik Garrison
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
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17
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Dzamba M, Ramani AK, Buczkowicz P, Jiang Y, Yu M, Hawkins C, Brudno M. Identification of complex genomic rearrangements in cancers using CouGaR. Genome Res 2016; 27:107-117. [PMID: 27986820 PMCID: PMC5204335 DOI: 10.1101/gr.211201.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/10/2016] [Indexed: 12/17/2022]
Abstract
The genomic alterations associated with cancers are numerous and varied, involving both isolated and large-scale complex genomic rearrangements (CGRs). Although the underlying mechanisms are not well understood, CGRs have been implicated in tumorigenesis. Here, we introduce CouGaR, a novel method for characterizing the genomic structure of amplified CGRs, leveraging both depth of coverage (DOC) and discordant pair-end mapping techniques. We applied our method to whole-genome sequencing (WGS) samples from The Cancer Genome Atlas and identify amplified CGRs in at least 5.2% (10+ copies) to 17.8% (6+ copies) of the samples. Furthermore, ∼95% of these amplified CGRs contain genes previously implicated in tumorigenesis, indicating the importance and widespread occurrence of CGRs in cancers. Additionally, CouGaR identified the occurrence of 'chromoplexy' in nearly 63% of all prostate cancer samples and 30% of all bladder cancer samples. To further validate the accuracy of our method, we experimentally tested 17 predicted fusions in two pediatric glioma samples and validated 15 of these (88%) with precise resolution of the breakpoints via qPCR experiments and Sanger sequencing, with nearly perfect copy count concordance. Additionally, to further help display and understand the structure of CGRs, we have implemented CouGaR-viz, a generic stand-alone tool for visualization of the copy count of regions, breakpoints, and relevant genes.
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Affiliation(s)
- Misko Dzamba
- Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 3G4, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Pawel Buczkowicz
- Division of Pathology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1E8, Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5G 1E8, Canada
| | - Yue Jiang
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Man Yu
- Division of Pathology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1E8, Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5G 1E8, Canada
| | - Cynthia Hawkins
- Division of Pathology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1E8, Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5G 1E8, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 3G4, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
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18
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Abstract
Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs-a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question remains: given a genome graph G (e.g., a de Bruijn, or a string graph), what are all the strings that can be safely reported from G as contigs? In this article, we answer this question using a model in which the genome is a circular covering walk. We also give a polynomial-time algorithm to find such strings, which we call omnitigs. Our experiments show that omnitigs are 66%-82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.
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Affiliation(s)
- Alexandru I Tomescu
- 1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki , Helsinki, Finland
| | - Paul Medvedev
- 2 Department of Computer Science and Engineering, The Pennsylvania State University , University Park, Pennsylvania.,3 Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania.,4 Department of Genome Sciences Institute of the Huck, The Pennsylvania State University , University Park, Pennsylvania
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19
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Gao S, Bertrand D, Chia BKH, Nagarajan N. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biol 2016; 17:102. [PMID: 27169502 PMCID: PMC4864936 DOI: 10.1186/s13059-016-0951-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
The assembly of large, repeat-rich eukaryotic genomes represents a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be expensive for larger genomes. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies. OPERA-LG provides an avenue for systematic augmentation and improvement of thousands of existing draft eukaryotic genome assemblies.
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Affiliation(s)
- Song Gao
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, Singapore, 117456, Singapore.,South Australian Health & Medical Research Institute, North Terrace, Adelaide, 5000, SA, Australia
| | - Denis Bertrand
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Burton K H Chia
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.
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20
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A Graph Extension of the Positional Burrows-Wheeler Transform and Its Applications. LECTURE NOTES IN COMPUTER SCIENCE 2016. [DOI: 10.1007/978-3-319-43681-4_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Boža V, Brejová B, Vinař T. GAML: genome assembly by maximum likelihood. Algorithms Mol Biol 2015; 10:18. [PMID: 26042154 PMCID: PMC4454275 DOI: 10.1186/s13015-015-0052-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly. Modern assemblers usually perform such steps by heuristics, often tailored to a particular technology for producing paired or long reads. RESULTS We propose a new framework that allows systematic combination of diverse sequencing datasets into a single assembly. We achieve this by searching for an assembly with the maximum likelihood in a probabilistic model capturing error rate, insert lengths, and other characteristics of the sequencing technology used to produce each dataset. We have implemented a prototype genome assembler GAML that can use any combination of insert sizes with Illumina or 454 reads, as well as PacBio reads. Our experiments show that we can assemble short genomes with N50 sizes and error rates comparable to ALLPATHS-LG or Cerulean. While ALLPATHS-LG and Cerulean require each a specific combination of datasets, GAML works on any combination. CONCLUSIONS We have introduced a new probabilistic approach to genome assembly and demonstrated that this approach can lead to superior results when used to combine diverse set of datasets from different sequencing technologies. Data and software is available at http://compbio.fmph.uniba.sk/gaml.
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Affiliation(s)
- Vladimír Boža
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Broňa Brejová
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Tomáš Vinař
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia
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22
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Abstract
The current genomic revolution was made possible by joint advances in genome sequencing technologies and computational approaches for analyzing sequence data. The close interaction between biologists and computational scientists is perhaps most apparent in the development of approaches for sequencing entire genomes, a feat that would not be possible without sophisticated computational tools called genome assemblers (short for genome sequence assemblers). Here, we survey the key developments in algorithms for assembling genome sequences since the development of the first DNA sequencing methods more than 35 years ago.
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Affiliation(s)
- Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada;
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23
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Abstract
Background Next generation sequencing (NGS) technologies have made it possible to exhaustively detect structural variations (SVs) in genomes. Although various methods for detecting SVs have been developed, the global structure of chromosomes, i.e., how segments in a reference genome are extracted and ordered in an unknown target genome, cannot be inferred by detecting only individual SVs. Results Here, we formulate the problem of inferring the global structure of chromosomes from SVs as an optimization problem on a bidirected graph. This problem takes into account the aberrant adjacencies of genomic regions, the copy numbers, and the number and length of chromosomes. Although the problem is NP-complete, we propose its polynomial-time solvable variation by restricting instances of the problem using a biologically meaningful condition, which we call the weakly connected constraint. We also explain how to obtain experimental data that satisfies the weakly connected constraint. Conclusion Our results establish a theoretical foundation for the development of practical computational tools that could be used to infer the global structure of chromosomes based on SVs. The computational complexity of the inference can be reduced by detecting the segments of the reference genome at the ends of the chromosomes of the target genome and also the segments that are known to exist in the target genome.
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24
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Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population. J Comput Biol 2015; 22:387-401. [PMID: 25565268 DOI: 10.1089/cmb.2014.0146] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homology into alignment blocks we formalize the problem of ordering and orienting the blocks such that the resulting ordering maximally agrees with the underlying genomes' ordering and orientation, creating a pan-genome reference ordering. We show this problem is NP-hard, but also demonstrate, empirically and within simulations, the performance of heuristic algorithms based upon a cactus graph decomposition to find locally maximal solutions. We describe an extension of our Cactus software to create a pan-genome reference for whole genome alignments, and demonstrate how it can be used to create novel genome browser visualizations using human variation data as a test. In addition, we test the use of a pan-genome for describing variations and as a reference for read mapping.
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Affiliation(s)
- Ngan Nguyen
- 1 Center for Biomolecular Science and Engineering, University of California , Santa Cruz, California
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25
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The complex task of choosing a de novo assembly: Lessons from fungal genomes. Comput Biol Chem 2014; 53 Pt A:97-107. [DOI: 10.1016/j.compbiolchem.2014.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 12/21/2022]
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26
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Ilie L, Haider B, Molnar M, Solis-Oba R. SAGE: String-overlap Assembly of GEnomes. BMC Bioinformatics 2014; 15:302. [PMID: 25225118 PMCID: PMC4174676 DOI: 10.1186/1471-2105-15-302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/01/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. RESULTS We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. CONCLUSIONS SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.
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Affiliation(s)
- Lucian Ilie
- Department of Computer Science, University of Western Ontario, N6A 5B7 London, Ontario Canada
| | - Bahlul Haider
- Department of Computer Science, University of Western Ontario, N6A 5B7 London, Ontario Canada
| | - Michael Molnar
- Department of Computer Science, University of Western Ontario, N6A 5B7 London, Ontario Canada
| | - Roberto Solis-Oba
- Department of Computer Science, University of Western Ontario, N6A 5B7 London, Ontario Canada
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27
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Abstract
BACKGROUND Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to orient, order, and link contigs into larger structures referred to as scaffolds. Due to library preparation artifacts and erroneous mapping of reads originating from repeats, scaffolding remains a challenging problem. In this paper, we provide a scalable scaffolding algorithm (SILP2) employing a maximum likelihood model capturing read mapping uncertainty and/or non-uniformity of contig coverage which is solved using integer linear programming. A Non-Serial Dynamic Programming (NSDP) paradigm is applied to render our algorithm useful in the processing of larger mammalian genomes. To compare scaffolding tools, we employ novel quantitative metrics in addition to the extant metrics in the field. We have also expanded the set of experiments to include scaffolding of low-complexity metagenomic samples. RESULTS SILP2 achieves better scalability throughg a more efficient NSDP algorithm than previous release of SILP. The results show that SILP2 compares favorably to previous methods OPERA and MIP in both scalability and accuracy for scaffolding single genomes of up to human size, and significantly outperforms them on scaffolding low-complexity metagenomic samples. CONCLUSIONS Equipped with NSDP, SILP2 is able to scaffold large mammalian genomes, resulting in the longest and most accurate scaffolds. The ILP formulation for the maximum likelihood model is shown to be flexible enough to handle metagenomic samples.
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Affiliation(s)
- James Lindsay
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Storrs, CT 06269-4155, USA
| | - Hamed Salooti
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, GA 30303, USA
| | - Ion Măndoiu
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Storrs, CT 06269-4155, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, GA 30303, USA
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28
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Bayesian genome assembly and assessment by markov chain monte carlo sampling. PLoS One 2014; 9:e99497. [PMID: 24968249 PMCID: PMC4072599 DOI: 10.1371/journal.pone.0099497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/15/2014] [Indexed: 11/26/2022] Open
Abstract
Most genome assemblers construct point estimates, choosing only a single genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. We implement this approach in a prototype assembler, called Genome Assembly by Bayesian Inference (GABI), and illustrate its application to the bacteriophage X174. Our sampling strategy achieves both good mixing and convergence on Illumina test data for X174, demonstrating the feasibility of our approach. We summarize the posterior distribution of assembly hypotheses generated by GABI as a majority-rule consensus assembly. Then we compare the posterior distribution to external assemblies of the same test data, and annotate those assemblies by assigning posterior probabilities to features that are in common with GABI’s assembly graph. GABI is freely available under a GPL license from https://bitbucket.org/mhowison/gabi.
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29
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Paten B, Zerbino DR, Hickey G, Haussler D. A unifying model of genome evolution under parsimony. BMC Bioinformatics 2014; 15:206. [PMID: 24946830 PMCID: PMC4082375 DOI: 10.1186/1471-2105-15-206] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 05/08/2014] [Indexed: 11/23/2022] Open
Abstract
Background Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. Results We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph G, a finite set of AVGs describe all parsimonious interpretations of G, and this set can be explored with a few sampling moves. Conclusion This theoretical study describes a model in which the inference of genome rearrangements and phylogeny can be unified under parsimony.
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Affiliation(s)
- Benedict Paten
- University of California, Santa Cruz, 1156 High St, 95064 Santa Cruz, USA.
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30
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Bernard E, Jacob L, Mairal J, Vert JP. Efficient RNA isoform identification and quantification from RNA-Seq data with network flows. Bioinformatics 2014; 30:2447-55. [PMID: 24813214 PMCID: PMC4147886 DOI: 10.1093/bioinformatics/btu317] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Motivation: Several state-of-the-art methods for isoform identification and quantification are based on ℓ1-regularized regression, such as the Lasso. However, explicitly listing the—possibly exponentially—large set of candidate transcripts is intractable for genes with many exons. For this reason, existing approaches using the ℓ1-penalty are either restricted to genes with few exons or only run the regression algorithm on a small set of preselected isoforms. Results: We introduce a new technique called FlipFlop, which can efficiently tackle the sparse estimation problem on the full set of candidate isoforms by using network flow optimization. Our technique removes the need of a preselection step, leading to better isoform identification while keeping a low computational cost. Experiments with synthetic and real RNA-Seq data confirm that our approach is more accurate than alternative methods and one of the fastest available. Availability and implementation: Source code is freely available as an R package from the Bioconductor Web site (http://www.bioconductor.org/), and more information is available at http://cbio.ensmp.fr/flipflop. Contact:Jean-Philippe.Vert@mines.org Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elsa Bernard
- Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France
| | - Laurent Jacob
- Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France
| | - Julien Mairal
- Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France
| | - Jean-Philippe Vert
- Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France
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31
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Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics 2014; 15:126. [PMID: 24884846 PMCID: PMC4030574 DOI: 10.1186/1471-2105-15-126] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/24/2014] [Indexed: 11/12/2022] Open
Abstract
Background The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. Results To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Conclusions Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.
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Affiliation(s)
- Sergey Koren
- National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA.
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Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ. Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res 2014; 24:697-707. [PMID: 24501022 PMCID: PMC3975068 DOI: 10.1101/gr.159624.113] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The human genome sequence remains incomplete, with multimegabase-sized gaps representing the endogenous centromeres and other heterochromatic regions. Available sequence-based studies within these sites in the genome have demonstrated a role in centromere function and chromosome pairing, necessary to ensure proper chromosome segregation during cell division. A common genomic feature of these regions is the enrichment of long arrays of near-identical tandem repeats, known as satellite DNAs, which offer a limited number of variant sites to differentiate individual repeat copies across millions of bases. This substantial sequence homogeneity challenges available assembly strategies and, as a result, centromeric regions are omitted from ongoing genomic studies. To address this problem, we utilize monomer sequence and ordering information obtained from whole-genome shotgun reads to model two haploid human satellite arrays on chromosomes X and Y, resulting in an initial characterization of 3.83 Mb of centromeric DNA within an individual genome. To further expand the utility of each centromeric reference sequence model, we evaluate sites within the arrays for short-read mappability and chromosome specificity. Because satellite DNAs evolve in a concerted manner, we use these centromeric assemblies to assess the extent of sequence variation among 366 individuals from distinct human populations. We thus identify two satellite array variants in both X and Y centromeres, as determined by array length and sequence composition. This study provides an initial sequence characterization of a regional centromere and establishes a foundation to extend genomic characterization to these sites as well as to other repeat-rich regions within complex genomes.
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Affiliation(s)
- Karen H Miga
- Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA
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El-Metwally S, Ouda OM, Helmy M. Approaches and Challenges of Next-Generation Sequence Assembly Stages. NEXT GENERATION SEQUENCING TECHNOLOGIES AND CHALLENGES IN SEQUENCE ASSEMBLY 2014. [DOI: 10.1007/978-1-4939-0715-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Orenstein Y, Shamir R. Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers. Bioinformatics 2013; 29:i71-9. [PMID: 23813011 PMCID: PMC3694677 DOI: 10.1093/bioinformatics/btt230] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Motivation: Novel technologies can generate large sets of short double-stranded DNA sequences that can be used to measure their regulatory effects. Microarrays can measure in vitro the binding intensity of a protein to thousands of probes. Synthetic enhancer sequences inserted into an organism’s genome allow us to measure in vivo the effect of such sequences on the phenotype. In both applications, by using sequence probes that cover all k-mers, a comprehensive picture of the effect of all possible short sequences on gene regulation is obtained. The value of k that can be used in practice is, however, severely limited by cost and space considerations. A key challenge is, therefore, to cover all k-mers with a minimal number of probes. The standard way to do this uses the de Bruijn sequence of length . However, as probes are double stranded, when a k-mer is included in a probe, its reverse complement k-mer is accounted for as well. Results: Here, we show how to efficiently create a shortest possible sequence with the property that it contains each k-mer or its reverse complement, but not necessarily both. The length of the resulting sequence approaches half that of the de Bruijn sequence as k increases resulting in a more efficient array, which allows covering more longer sequences; alternatively, additional sequences with redundant k-mers of interest can be added. Availability: The software is freely available from our website http://acgt.cs.tau.ac.il/shortcake/. Contact:rshamir@tau.ac.il
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Affiliation(s)
- Yaron Orenstein
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel
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El-Metwally S, Hamza T, Zakaria M, Helmy M. Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol 2013; 9:e1003345. [PMID: 24348224 PMCID: PMC3861042 DOI: 10.1371/journal.pcbi.1003345] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still remains a major challenge. In this review, we address the basic framework of next-generation genome sequence assemblers, which comprises four basic stages: preprocessing filtering, a graph construction process, a graph simplification process, and postprocessing filtering. Here we discuss them as a framework of four stages for data analysis and processing and survey variety of techniques, algorithms, and software tools used during each stage. We also discuss the challenges that face current assemblers in the next-generation environment to determine the current state-of-the-art. We recommend a layered architecture approach for constructing a general assembler that can handle the sequences generated by different sequencing platforms.
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Affiliation(s)
- Sara El-Metwally
- Computer Science Department, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | - Taher Hamza
- Computer Science Department, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | - Magdi Zakaria
- Computer Science Department, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | - Mohamed Helmy
- Botany Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
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Howison M, Zapata F, Dunn CW. Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics 2013; 29:2959-63. [PMID: 24021385 DOI: 10.1093/bioinformatics/btt525] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Draft de novo genome assemblies are now available for many organisms. These assemblies are point estimates of the true genome sequences. Each is a specific hypothesis, drawn from among many alternative hypotheses, of the sequence of a genome. Assembly uncertainty, the inability to distinguish between multiple alternative assembly hypotheses, can be due to real variation between copies of the genome in the sample, errors and ambiguities in the sequenced data and assumptions and heuristics of the assemblers. Most assemblers select a single assembly according to ad hoc criteria, and do not yet report and quantify the uncertainty of their outputs. Those assemblers that do report uncertainty take different approaches to describing multiple assembly hypotheses and the support for each. RESULTS Here we review and examine the problem of representing and measuring uncertainty in assemblies. A promising recent development is the implementation of assemblers that are built according to explicit statistical models. Some new assembly methods, for example, estimate and maximize assembly likelihood. These advances, combined with technical advances in the representation of alternative assembly hypotheses, will lead to a more complete and biologically relevant understanding of assembly uncertainty. This will in turn facilitate the interpretation of downstream analyses and tests of specific biological hypotheses.
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Affiliation(s)
- Mark Howison
- Center for Computation and Visualization and Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
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Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for comparing genome assemblies. BMC Res Notes 2013; 6:334. [PMID: 23965294 PMCID: PMC3765854 DOI: 10.1186/1756-0500-6-334] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/13/2013] [Indexed: 12/12/2022] Open
Abstract
Background The current revolution in genomics has been made possible by software tools called genome assemblers, which stitch together DNA fragments “read” by sequencing machines into complete or nearly complete genome sequences. Despite decades of research in this field and the development of dozens of genome assemblers, assessing and comparing the quality of assembled genome sequences still relies on the availability of independently determined standards, such as manually curated genome sequences, or independently produced mapping data. These “gold standards” can be expensive to produce and may only cover a small fraction of the genome, which limits their applicability to newly generated genome sequences. Here we introduce a de novo probabilistic measure of assembly quality which allows for an objective comparison of multiple assemblies generated from the same set of reads. We define the quality of a sequence produced by an assembler as the conditional probability of observing the sequenced reads from the assembled sequence. A key property of our metric is that the true genome sequence maximizes the score, unlike other commonly used metrics. Results We demonstrate that our de novo score can be computed quickly and accurately in a practical setting even for large datasets, by estimating the score from a relatively small sample of the reads. To demonstrate the benefits of our score, we measure the quality of the assemblies generated in the GAGE and Assemblathon 1 assembly “bake-offs” with our metric. Even without knowledge of the true reference sequence, our de novo metric closely matches the reference-based evaluation metrics used in the studies and outperforms other de novo metrics traditionally used to measure assembly quality (such as N50). Finally, we highlight the application of our score to optimize assembly parameters used in genome assemblers, which enables better assemblies to be produced, even without prior knowledge of the genome being assembled. Conclusion Likelihood-based measures, such as ours proposed here, will become the new standard for de novo assembly evaluation.
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Affiliation(s)
- Mohammadreza Ghodsi
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
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Abstract
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on earlier works, we design a de Brujin graph based assembly algorithm which can achieve very close to the lower bound for repeat statistics of a wide range of sequenced genomes, including the GAGE datasets. The results are based on a set of necessary and sufficient conditions on the DNA sequence and the reads for reconstruction. The conditions can be viewed as the shotgun sequencing analogue of Ukkonen-Pevzner's necessary and sufficient conditions for Sequencing by Hybridization.
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Abstract
De Bruijn Superwalk with Multiplicities Problem is the problem of finding a walk in the de Bruijn graph containing several walks as subwalks and passing through each edge the exactly predefined number of times (equal to the multiplicity of this edge). This problem has been stated in the talk by Paul Medvedev and Michael Brudno on the first RECOMB Satellite Conference on Open Problems in Algorithmic Biology in August 2012. In this paper we show that this problem is NP-hard. Combined with results of previous works it means that all known models for genome assembly are NP-hard.
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Affiliation(s)
- Evgeny Kapun
- St. Petersburg National Research University of Information Technologies, Mechanics and Optics Genome Assembly Algorithms Laboratory, Kronverksky pr. 49, St. Petersburg, Russia
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Rahman A, Pachter L. CGAL: computing genome assembly likelihoods. Genome Biol 2013; 14:R8. [PMID: 23360652 PMCID: PMC3663106 DOI: 10.1186/gb-2013-14-1-r8] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/29/2013] [Indexed: 01/12/2023] Open
Abstract
Assembly algorithms have been extensively benchmarked using simulated data so that results can be compared to ground truth. However, in de novo assembly, only crude metrics such as contig number and size are typically used to evaluate assembly quality. We present CGAL, a novel likelihood-based approach to assembly assessment in the absence of a ground truth. We show that likelihood is more accurate than other metrics currently used for evaluating assemblies, and describe its application to the optimization and comparison of assembly algorithms. Our methods are implemented in software that is freely available at http://bio.math.berkeley.edu/cgal/.
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Kapun E, Tsarev F. On NP-Hardness of the Paired de Bruijn Sound Cycle Problem. LECTURE NOTES IN COMPUTER SCIENCE 2013. [DOI: 10.1007/978-3-642-40453-5_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Nijkamp JF, van den Broek MA, Geertman JMA, Reinders MJT, Daran JMG, de Ridder D. De novo detection of copy number variation by co-assembly. Bioinformatics 2012; 28:3195-202. [DOI: 10.1093/bioinformatics/bts601] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Bashir A, Klammer A, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol 2012; 30:701-707. [PMID: 22750883 DOI: 10.1038/nbt.2288] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/30/2012] [Indexed: 02/08/2023]
Abstract
Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at >99.9% accuracy. Complex regions with clinically relevant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 cholera reference strain, we obtained 14 scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of greater than 1 kb for the simulated data, which allowed us to correct several errors in contigs assembled from the short-read data alone. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lori Rowe
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta GA 30333
| | - Michael Frace
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta GA 30333
| | - Cheryl L Tarr
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta GA 30333
| | - Maryann Turnsek
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta GA 30333
| | - Brigid M Davis
- Channing Laboratory, Brigham and Women's Hospital, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA.,Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA.,Howard Hughes Medical Institute, Boston, MA
| | | | | | - Matthew K Waldor
- Channing Laboratory, Brigham and Women's Hospital, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA.,Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA.,Howard Hughes Medical Institute, Boston, MA
| | - Eric E Schadt
- Pacific Biosciences, Menlo Park, CA.,Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City
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Sahli M, Shibuya T. Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes. BMC Res Notes 2012; 5:243. [PMID: 22591859 PMCID: PMC3441218 DOI: 10.1186/1756-0500-5-243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 05/16/2012] [Indexed: 11/12/2022] Open
Abstract
Background Genome assembly is considered to be a challenging problem in computational biology, and has been studied extensively by many researchers. It is extremely difficult to build a general assembler that is able to reconstruct the original sequence instead of many contigs. However, we believe that creating specific assemblers, for solving specific cases, will be much more fruitful than creating general assemblers. Findings In this paper, we present Arapan-S, a whole-genome assembly program dedicated to handling small genomes. It provides only one contig (along with the reverse complement of this contig) in many cases. Although genomes consist of a number of segments, the implemented algorithm can detect all the segments, as we demonstrate for Influenza Virus A. The Arapan-S program is based on the de Bruijn graph. We have implemented a very sophisticated and fast method to reconstruct the original sequence and neglect erroneous k-mers. The method explores the graph by using neither the shortest nor the longest path, but rather a specific and reliable path based on the coverage level or k-mers’ lengths. Arapan-S uses short reads, and it was tested on raw data downloaded from the NCBI Trace Archive. Conclusions Our findings show that the accuracy of the assembly was very high; the result was checked against the European Bioinformatics Institute (EBI) database using the NCBI BLAST Sequence Similarity Search. The identity and the genome coverage was more than 99%. We also compared the efficiency of Arapan-S with other well-known assemblers. In dealing with small genomes, the accuracy of Arapan-S is significantly higher than the accuracy of other assemblers. The assembly process is very fast and requires only a few seconds. Arapan-S is available for free to the public. The binary files for Arapan-S are available through http://sourceforge.net/projects/dnascissor/files/.
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Affiliation(s)
- Mohammed Sahli
- Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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Abstract
Background A cancer genome is derived from the germline genome through a series of somatic mutations. Somatic structural variants - including duplications, deletions, inversions, translocations, and other rearrangements - result in a cancer genome that is a scrambling of intervals, or "blocks" of the germline genome sequence. We present an efficient algorithm for reconstructing the block organization of a cancer genome from paired-end DNA sequencing data. Results By aligning paired reads from a cancer genome - and a matched germline genome, if available - to the human reference genome, we derive: (i) a partition of the reference genome into intervals; (ii) adjacencies between these intervals in the cancer genome; (iii) an estimated copy number for each interval. We formulate the Copy Number and Adjacency Genome Reconstruction Problem of determining the cancer genome as a sequence of the derived intervals that is consistent with the measured adjacencies and copy numbers. We design an efficient algorithm, called Paired-end Reconstruction of Genome Organization (PREGO), to solve this problem by reducing it to an optimization problem on an interval-adjacency graph constructed from the data. The solution to the optimization problem results in an Eulerian graph, containing an alternating Eulerian tour that corresponds to a cancer genome that is consistent with the sequencing data. We apply our algorithm to five ovarian cancer genomes that were sequenced as part of The Cancer Genome Atlas. We identify numerous rearrangements, or structural variants, in these genomes, analyze reciprocal vs. non-reciprocal rearrangements, and identify rearrangements consistent with known mechanisms of duplication such as tandem duplications and breakage/fusion/bridge (B/F/B) cycles. Conclusions We demonstrate that PREGO efficiently identifies complex and biologically relevant rearrangements in cancer genome sequencing data. An implementation of the PREGO algorithm is available at http://compbio.cs.brown.edu/software/.
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Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HOK, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011; 21:2224-41. [PMID: 21926179 DOI: 10.1101/gr.126599.111] [Citation(s) in RCA: 318] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.
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Affiliation(s)
- Dent Earl
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
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47
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Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HOK, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011. [PMID: 21926179 DOI: 10.1101/gr.126599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.
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Affiliation(s)
- Dent Earl
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
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Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment. Genome Res 2011; 21:1512-28. [PMID: 21665927 DOI: 10.1101/gr.123356.111] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new "Cactus" alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.
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Affiliation(s)
- Benedict Paten
- Center for Biomolecular Science and Engineering, University of California-Santa Cruz, CA 95064, USA.
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Wetzel J, Kingsford C, Pop M. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 2011; 12:95. [PMID: 21486487 PMCID: PMC3103447 DOI: 10.1186/1471-2105-12-95] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 04/13/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-generation sequencing technologies allow genomes to be sequenced more quickly and less expensively than ever before. However, as sequencing technology has improved, the difficulty of de novo genome assembly has increased, due in large part to the shorter reads generated by the new technologies. The use of mated sequences (referred to as mate-pairs) is a standard means of disambiguating assemblies to obtain a more complete picture of the genome without resorting to manual finishing. Here, we examine the effectiveness of mate-pair information in resolving repeated sequences in the DNA (a paramount issue to overcome). While it has been empirically accepted that mate-pairs improve assemblies, and a variety of assemblers use mate-pairs in the context of repeat resolution, the effectiveness of mate-pairs in this context has not been systematically evaluated in previous literature. RESULTS We show that, in high-coverage prokaryotic assemblies, libraries of short mate-pairs (about 4-6 times the read-length) more effectively disambiguate repeat regions than the libraries that are commonly constructed in current genome projects. We also demonstrate that the best assemblies can be obtained by 'tuning' mate-pair libraries to accommodate the specific repeat structure of the genome being assembled - information that can be obtained through an initial assembly using unpaired reads. These results are shown across 360 simulations on 'ideal' prokaryotic data as well as assembly of 8 bacterial genomes using SOAPdenovo. The simulation results provide an upper-bound on the potential value of mate-pairs for resolving repeated sequences in real prokaryotic data sets. The assembly results show that our method of tuning mate-pairs exploits fundamental properties of these genomes, leading to better assemblies even when using an off -the-shelf assembler in the presence of base-call errors. CONCLUSIONS Our results demonstrate that dramatic improvements in prokaryotic genome assembly quality can be achieved by tuning mate-pair sizes to the actual repeat structure of a genome, suggesting the possible need to change the way sequencing projects are designed. We propose that a two-tiered approach - first generate an assembly of the genome with unpaired reads in order to evaluate the repeat structure of the genome; then generate the mate-pair libraries that provide most information towards the resolution of repeats in the genome being assembled - is not only possible, but likely also more cost-effective as it will significantly reduce downstream manual finishing costs. In future work we intend to address the question of whether this result can be extended to larger eukaryotic genomes, where repeat structure can be quite different.
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Affiliation(s)
- Joshua Wetzel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
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Miller CA, Buckley KM, Easley RL, Smith LC. An Sp185/333 gene cluster from the purple sea urchin and putative microsatellite-mediated gene diversification. BMC Genomics 2010; 11:575. [PMID: 20955585 PMCID: PMC3091723 DOI: 10.1186/1471-2164-11-575] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 10/18/2010] [Indexed: 11/19/2022] Open
Abstract
Background The immune system of the purple sea urchin, Strongylocentrotus purpuratus, is complex and sophisticated. An important component of sea urchin immunity is the Sp185/333 gene family, which is significantly upregulated in immunologically challenged animals. The Sp185/333 genes are less than 2 kb with two exons and are members of a large diverse family composed of greater than 40 genes. The S. purpuratus genome assembly, however, contains only six Sp185/333 genes. This underrepresentation could be due to the difficulties that large gene families present in shotgun assembly, where multiple similar genes can be collapsed into a single consensus gene. Results To understand the genomic organization of the Sp185/333 gene family, a BAC insert containing Sp185/333 genes was assembled, with careful attention to avoiding artifacts resulting from collapse or artificial duplication/expansion of very similar genes. Twelve candidate BAC assemblies were generated with varying parameters and the optimal assembly was identified by PCR, restriction digests, and subclone sequencing. The validated assembly contained six Sp185/333 genes that were clustered in a 34 kb region at one end of the BAC with five of the six genes tightly clustered within 20 kb. The Sp185/333 genes in this cluster were no more similar to each other than to previously sequenced Sp185/333 genes isolated from three different animals. This was unexpected given their proximity and putative effects of gene homogenization in closely linked, similar genes. All six genes displayed significant similarity including both 5' and 3' flanking regions, which were bounded by microsatellites. Three of the Sp185/333 genes and their flanking regions were tandemly duplicated such that each repeated segment consisted of a gene plus 0.7 kb 5' and 2.4 kb 3' of the gene (4.5 kb total). Both edges of the segmental duplications were bounded by different microsatellites. Conclusions The high sequence similarity of the Sp185/333 genes and flanking regions, suggests that the microsatellites may promote genomic instability and are involved with gene duplication and/or gene conversion and the extraordinary sequence diversity of this family.
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Affiliation(s)
- Chase A Miller
- Genomics and Bioinformatics Program, Department of Biochemistry, Schoolof Medicine, The George Washington University, Washington, DC 20037, USA
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