MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Identifieur interne : 000364 ( Ncbi/Curation ); précédent : 000363; suivant : 000365MOCAT: 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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PMC:3474746Le document en format XML
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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>
.</p>
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<biblStruct><analytic><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name>
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