MOCAT2: A metagenomic assembly, annotation and profiling framework

Jens Roat Kultima; Luis Pedro Coelho; Kristoffer Forslund; Jaime Huerta-Cepas; Simone S. Li; Marja Driessen; Anita Yvonne Voigt; Georg Zeller; Shinichi Sunagawa; Peer Bork

doi:10.1093/bioinformatics/btw183

MOCAT2: A metagenomic assembly, annotation and profiling framework

Jens Roat Kultima
, Luis Pedro Coelho
, Kristoffer Forslund
, Jaime Huerta-Cepas
, Simone S. Li
, Marja Driessen
, Anita Yvonne Voigt
, Georg Zeller
, Shinichi Sunagawa
, Peer Bork

Research output: Contribution to journal › Article › Research › peer-review

155 Citations (Scopus)

Abstract

Summary: MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. Availability and Implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de.

Original language	English
Pages (from-to)	2520-2523
Number of pages	4
Journal	Bioinformatics
Volume	32
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/btw183
Publication status	Published - Aug 2016
Externally published	Yes

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10.1093/bioinformatics/btw183Licence: CC BY-NC

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title = "MOCAT2: A metagenomic assembly, annotation and profiling framework",

abstract = "Summary: MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. Availability and Implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de.",

author = "Kultima, \{Jens Roat\} and Coelho, \{Luis Pedro\} and Kristoffer Forslund and Jaime Huerta-Cepas and Li, \{Simone S.\} and Marja Driessen and Voigt, \{Anita Yvonne\} and Georg Zeller and Shinichi Sunagawa and Peer Bork",

note = "Funding Information: This work was supported by the European Research Council CancerBiome project [grant number 268985], the International Human Microbiome Standards project [grant number HEALTH-2010-261376] and the MetaCardis project [grant number HEALTH-2012-305312]. S.S.L. is the recipient of an Australian Postgraduate Award and EMBL Australia International PhD Fellowship. Publisher Copyright: {\textcopyright} 2016 The Author 2016. Published by Oxford University Press.",

year = "2016",

month = aug,

doi = "10.1093/bioinformatics/btw183",

language = "English",

volume = "32",

pages = "2520--2523",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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T2 - A metagenomic assembly, annotation and profiling framework

AU - Kultima, Jens Roat

AU - Coelho, Luis Pedro

AU - Forslund, Kristoffer

AU - Huerta-Cepas, Jaime

AU - Li, Simone S.

AU - Driessen, Marja

AU - Voigt, Anita Yvonne

AU - Zeller, Georg

AU - Sunagawa, Shinichi

AU - Bork, Peer

N1 - Funding Information: This work was supported by the European Research Council CancerBiome project [grant number 268985], the International Human Microbiome Standards project [grant number HEALTH-2010-261376] and the MetaCardis project [grant number HEALTH-2012-305312]. S.S.L. is the recipient of an Australian Postgraduate Award and EMBL Australia International PhD Fellowship. Publisher Copyright: © 2016 The Author 2016. Published by Oxford University Press.

PY - 2016/8

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N2 - Summary: MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. Availability and Implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de.

AB - Summary: MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. Availability and Implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de.

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JO - Bioinformatics

JF - Bioinformatics

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ER -

MOCAT2: A metagenomic assembly, annotation and profiling framework

Abstract

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