Dataset Information

MOCAT: a metagenomics assembly and gene prediction toolkit.

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 http://www.bork.embl.de/mocat/.

SUBMITTER: Kultima JR

PROVIDER: S-EPMC3474746 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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MOCAT: a metagenomics assembly and gene prediction toolkit.

Kultima Jens Roat JR Sunagawa Shinichi S Li Junhua J Chen Weineng W Chen Hua H Mende Daniel R DR Arumugam Manimozhiyan M Pan Qi Q Liu Binghang B Qin Junjie J Wang Jun J Wang Jun J Bork Peer P

PloS one 20121017 10

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. Relevan ...[more]

PMID: 23082188

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Dataset Information

MOCAT: a metagenomics assembly and gene prediction toolkit.

Publications

MOCAT: a metagenomics assembly and gene prediction toolkit.

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