Sequence assembly with CAFTOOLS

Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data

With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data formats have been produced to accommodate different sequencing equipment providers or analytical software. However, the data interoperability between these tools brings great challenges to researchers. A generic format that could be shared by most of the software and tools in the NGS field would make data interoperability and sharing easier. In this paper, we defined a general XML-based NGS markup language (NGSML) format for the representation and exchange of NGS data. We also developed a user-friendly GUI tool, NGSMLEditor, for presenting, creating, editing, and converting NGSML files. By using NGSML, various types of NGS data can be saved in one unified format. Compared with the unstructured plain text file, a structured data format based on XML technology solves the incompatibility of various NGS data formats. The NGSML specifications are freely available from http://www.sysbio.org.cn/NGSML. NGSMLEditor is open source under GNU GPL and can be downloaded from the website.

Gap5--editing the billion fragment sequence assembly

Motivation: Existing sequence assembly editors struggle with the volumes of data now readily available from the latest generation of DNA sequencing instruments.

Results: We describe the Gap5 software along with the data structures and algorithms used that allow it to be scalable. We demonstrate this with an assembly of 1.1 billion sequence fragments and compare the performance with several other programs. We analyse the memory, CPU, I/O usage and file sizes used by Gap5.

Availability and Implementation: Gap5 is part of the Staden Package and is available under an Open Source licence from http://staden.sourceforge.net. It is implemented in C and Tcl/Tk. Currently it works on Unix systems only.

Contact:jkb@sanger.ac.uk

Supplementary information:Supplementary data are available at Bioinformatics online.

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis

BACKGROUND

Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood.

METHODOLOGY/PRINCIPAL FINDINGS

The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, approximately 40% of the approximately 2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three approximately 90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors.

CONCLUSIONS/SIGNIFICANCE

The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.

Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs

We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring in different variations thereof. The assembler uses iterative multipass strategies centered on high-confidence regions within sequences and has a fallback strategy for using low-confidence regions when needed. It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that edits and analyzes alignments by inspecting the underlying traces, and detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence. In addition, it includes possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information such as base-error probabilities, template insert sizes, strain information, etc., and functions to detect and resolve possible misassemblies. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.

Gene discovery and gene function assignment in filamentous fungi

Filamentous fungi are a large group of diverse and economically important microorganisms. Large-scale gene disruption strategies developed in budding yeast are not applicable to these organisms because of their larger genomes and lower rate of targeted integration (TI) during transformation. We developed transposon-arrayed gene knockouts (TAGKO) to discover genes and simultaneously create gene disruption cassettes for subsequent transformation and mutant analysis. Transposons carrying a bacterial and fungal drug resistance marker are used to mutagenize individual cosmids or entire libraries in vitro. Cosmids are annotated by DNA sequence analysis at the transposon insertion sites, and cosmid inserts are liberated to direct insertional mutagenesis events in the genome. Based on saturation analysis of a cosmid insert and insertions in a fungal cosmid library, we show that TAGKO can be used to rapidly identify and mutate genes. We further show that insertions can create alterations in gene expression, and we have used this approach to investigate an amino acid oxidation pathway in two important fungal phytopathogens.

Characterization of five novel human genes in the 11q13-q22 region

The redundancy of sequences in dbEST has approached a level where contiguous cDNA sequences of genes can be assembled, without the need to physically handle the clones from which the ESTs are derived. This is termed EST based in silico gene cloning. With the availability of sequence chromatogram files for a subset of ESTs, the quality of EST sequences can be ascertained accurately and used in contig assembly. In this report, we performed a study using this approach and isolated five novel human genes, C11orf1-C11orf5, in the 11q13-q22 region. The full open reading frames of these genes were determined by comparison with their orthologs, of which four mouse orthologs were isolated (c11orf1, c11orf2, c11orf3 and c11orf5). These genes were then analyzed using several proteomics tools. Both C11orf1 and C11orf2 are nuclear proteins with no other distinguishing features. C11orf3 is a cytoplasmic protein containing an ATP/GTP binding site, a signal peptide located in the N-terminus and a similarity to the C. elegans protein "Probable ARP 2/3 complex 20kD subunit." C11orf4 is a peptide which displays four putative transmembrane domains and is predicted to have a cytoplasmic localization. It contains signal peptides at the N- and C-termini. C11orf5 is a putative nuclear protein displaying a central coiled coil domain. Here, we propose that this purely EST-based cloning approach can be used by modestly sized laboratories to rapidly and accurately characterize and map a significant number of human genes without the need of further sequencing.

Genome sequence of the nematode C. elegans: a platform for investigating biology

The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms. There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly conserved genes provides evidence for a regional organization of the chromosomes.

Toward a complete human genome sequence

We have begun a joint program as part of a coordinated international effort to determine a complete human genome sequence. Our strategy is to map large-insert bacterial clones and to sequence each clone by a random shotgun approach followed by directed finishing. As of September 1998, we have identified the map positions of bacterial clones covering approximately 860 Mb for sequencing and completed >98 Mb ( approximately 3.3%) of the human genome sequence. Our progress and sequencing data can be accessed via the World Wide Web (http://webace.sanger.ac.uk/HGP/ or http://genome.wustl.edu/gsc/).