MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Identifieur interne : 000611 ( Pmc/Curation ); précédent : 000610; suivant : 000612MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Auteurs : Jens Roat Kultima [Allemagne] ; Shinichi Sunagawa [Allemagne] ; Junhua Li [République populaire de Chine] ; Weineng Chen [République populaire de Chine] ; Hua Chen [République populaire de Chine] ; Daniel R. Mende [Allemagne] ; Manimozhiyan Arumugam [Allemagne] ; Qi Pan [République populaire de Chine] ; Binghang Liu [République populaire de Chine] ; Junjie Qin [République populaire de Chine] ; Jun Wang [République populaire de Chine] ; Peer Bork [Allemagne]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at
Url:
DOI: 10.1371/journal.pone.0047656
PubMed: 23082188
PubMed Central: 3474746
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<front><div type="abstract" xml:lang="en"><p>MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at <ext-link ext-link-type="uri" xlink:href="http://www.bork.embl.de/mocat/">http://www.bork.embl.de/mocat/</ext-link>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23082188</article-id>
<article-id pub-id-type="pmc">3474746</article-id>
<article-id pub-id-type="publisher-id">PONE-D-12-19380</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0047656</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Analysis Tools</subject>
<subj-group><subject>Gene Prediction</subject>
<subject>Sequence Assembly Tools</subject>
</subj-group>
</subj-group>
<subj-group><subject>Comparative Genomics</subject>
<subject>Metagenomics</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group><subject>Ecology</subject>
<subj-group><subject>Community Ecology</subject>
<subj-group><subject>Community Assembly</subject>
<subject>Community Structure</subject>
</subj-group>
</subj-group>
<subj-group><subject>Microbial Ecology</subject>
</subj-group>
</subj-group>
<subj-group><subject>Microbiology</subject>
<subj-group><subject>Microbial Ecology</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit</article-title>
<alt-title alt-title-type="running-head">MOCAT: Metagenomics Toolkit</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Kultima</surname>
<given-names>Jens Roat</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author" equal-contrib="yes"><name><surname>Sunagawa</surname>
<given-names>Shinichi</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Junhua</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Weineng</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Hua</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mende</surname>
<given-names>Daniel R.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Arumugam</surname>
<given-names>Manimozhiyan</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pan</surname>
<given-names>Qi</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Liu</surname>
<given-names>Binghang</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Qin</surname>
<given-names>Junjie</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wang</surname>
<given-names>Jun</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bork</surname>
<given-names>Peer</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line>
</aff>
<aff id="aff3"><label>3</label>
<addr-line>School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, Guangdong, China</addr-line>
</aff>
<aff id="aff4"><label>4</label>
<addr-line>Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch, Germany</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Gilbert</surname>
<given-names>Jack Anthony</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Argonne National Laboratory, United States of America</addr-line>
</aff>
<author-notes><corresp id="cor1">* E-mail: <email>bork@embl.de</email>
</corresp>
<fn fn-type="conflict"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con"><p>Conceived and designed the experiments: JRK SS PB. Performed the experiments: JRK SS. Analyzed the data: JRK SS. Contributed reagents/materials/analysis tools: DRM MA JL WC HC QP BL JQ JW. Wrote the paper: JRK SS PB.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>10</month>
<year>2012</year>
</pub-date>
<volume>7</volume>
<issue>10</issue>
<elocation-id>e47656</elocation-id>
<history><date date-type="received"><day>27</day>
<month>6</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>13</day>
<month>9</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-year>2012</copyright-year>
<copyright-holder>Kultima et al</copyright-holder>
<license><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract><p>MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at <ext-link ext-link-type="uri" xlink:href="http://www.bork.embl.de/mocat/">http://www.bork.embl.de/mocat/</ext-link>
.</p>
</abstract>
<funding-group><funding-statement>This work was funded by EMBL, the European Community’s Seventh Framework Programme via the MetaHIT (HEALTH-F4-2007-201052), International Human Microbiome Standards (IHMS) (HEALTH-F4-2010-261376), and Cancerbiome (ERC Advanced Grant 268985) grants. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><page-count count="6"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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