| Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer. | |
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MedLine Citation:
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PMID: 23199210 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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New sequencing platforms have enabled rapid decoding of complete prokaryotic genomes at relatively low cost. The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. One particular problem is the lack of genomes that enable reference-based assembly, such as the one used in the present study, Corynebacterium pseudotuberculosis biovar equi, which causes high economic losses in the US equine industry. The quality treatment strategy incorporated into the assembly pipeline enabled a 16-fold greater use of the sequencing data obtained compared with traditional quality filter approaches. Data preprocessing prior to the de novo assembly enabled the use of known methodologies in the next-generation sequencing data assembly. Moreover, manual curation was proved to be essential for ensuring a quality assembly, which was validated by comparative genomics with other species of the genus Corynebacterium. The present study presents a modus operandi that enables a greater and better use of data obtained from semiconductor sequencing for obtaining the complete genome from a prokaryotic microorganism, C. pseudotuberculosis, which is not a traditional biological model such as Escherichia coli. |
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Authors:
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Rommel Thiago Jucá Ramos; Adriana Ribeiro Carneiro; Siomar de Castro Soares; Anderson Rodrigues Dos Santos; Sintia Almeida; Luis Guimarães; Flávia Figueira; Eudes Barbosa; Andreas Tauch; Vasco Azevedo; Artur Silva |
Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-12-2 |
Journal Detail:
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Title: Microbial biotechnology Volume: - ISSN: 1751-7915 ISO Abbreviation: Microb Biotechnol Publication Date: 2012 Dec |
Date Detail:
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Created Date: 2012-12-3 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101316335 Medline TA: Microb Biotechnol Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Copyright Information:
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© 2012 The Authors. Published by Society for Applied Microbiology and Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
Affiliation:
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Institute of Biological Sciences, Federal University Pará, Belém, Pará, Brazil. |
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