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Mariano DCB, Pereira FL, Aguiar EL, Oliveira LC, Benevides L, Guimarães LC, Folador EL, Sousa TJ, Ghosh P, Barh D, Figueiredo HCP, Silva A, Ramos RTJ, Azevedo VAC. SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology. BMC Bioinformatics 2016; 17:456. [PMID: 28105921 PMCID: PMC5249034 DOI: 10.1186/s12859-016-1344-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. RESULTS In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. CONCLUSION Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .
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Affiliation(s)
- Diego C. B. Mariano
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Felipe L. Pereira
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edgar L. Aguiar
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Letícia C. Oliveira
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Leandro Benevides
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Luís C. Guimarães
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edson L. Folador
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Thiago J. Sousa
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Preetam Ghosh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
| | - Henrique C. P. Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Rommel T. J. Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Vasco A. C. Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
- Federal University of Minas Gerais, Institute of Biological Sciences, Antônio Carlos 6627, Pampulha, 30161-970 Belo Horizonte, Minas Gerais Brazil
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Mariano DCB, Sousa TDJ, Pereira FL, Aburjaile F, Barh D, Rocha F, Pinto AC, Hassan SS, Saraiva TDL, Dorella FA, de Carvalho AF, Leal CAG, Figueiredo HCP, Silva A, Ramos RTJ, Azevedo VAC. Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002. BMC Genomics 2016; 17:315. [PMID: 27129708 PMCID: PMC4851793 DOI: 10.1186/s12864-016-2673-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/22/2016] [Indexed: 12/13/2022] Open
Abstract
Background Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements. Results In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions. Conclusion In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2673-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diego César Batista Mariano
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Luiz Pereira
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, 721172, India
| | - Flávia Rocha
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Anne Cybelle Pinto
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Syed Shah Hassan
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Tessália Diniz Luerce Saraiva
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Alves Dorella
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Alex Fiorini de Carvalho
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Augusto Gomes Leal
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique César Pereira Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Vasco Ariston Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
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Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01673-15. [PMID: 26823597 PMCID: PMC4732350 DOI: 10.1128/genomea.01673-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present the complete genome sequence of Corynebacterium pseudotuberculosis strain N1. The sequencing was performed with the Ion Torrent Personal Genome Machine system. The genome is a circular chromosome with 2,337,845 bp, a G+C content of 52.85%, and a total of 2,045 coding sequences, 12 rRNAs, 49 tRNAs, and 58 pseudogenes.
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