MOCAT2: a metagenomic assembly, annotation and profiling framework

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 dat...

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Autores principales: Kultima, Jens Roat, Coelho, Luis Pedro, Forslund, Kristoffer, Huerta-Cepas, Jaime, Li, Simone S., Driessen, Marja, Voigt, Anita Yvonne, Zeller, Georg, Sunagawa, Shinichi, Bork, Peer
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978931/
https://www.ncbi.nlm.nih.gov/pubmed/27153620
http://dx.doi.org/10.1093/bioinformatics/btw183
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author Kultima, Jens Roat
Coelho, Luis Pedro
Forslund, Kristoffer
Huerta-Cepas, Jaime
Li, Simone S.
Driessen, Marja
Voigt, Anita Yvonne
Zeller, Georg
Sunagawa, Shinichi
Bork, Peer
author_facet Kultima, Jens Roat
Coelho, Luis Pedro
Forslund, Kristoffer
Huerta-Cepas, Jaime
Li, Simone S.
Driessen, Marja
Voigt, Anita Yvonne
Zeller, Georg
Sunagawa, Shinichi
Bork, Peer
author_sort Kultima, Jens Roat
collection PubMed
description 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. Contact: bork@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-49789312016-08-11 MOCAT2: a metagenomic assembly, annotation and profiling framework Kultima, Jens Roat Coelho, Luis Pedro Forslund, Kristoffer Huerta-Cepas, Jaime Li, Simone S. Driessen, Marja Voigt, Anita Yvonne Zeller, Georg Sunagawa, Shinichi Bork, Peer Bioinformatics Applications Notes 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. Contact: bork@embl.de Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2016-08-15 2016-04-08 /pmc/articles/PMC4978931/ /pubmed/27153620 http://dx.doi.org/10.1093/bioinformatics/btw183 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Kultima, Jens Roat
Coelho, Luis Pedro
Forslund, Kristoffer
Huerta-Cepas, Jaime
Li, Simone S.
Driessen, Marja
Voigt, Anita Yvonne
Zeller, Georg
Sunagawa, Shinichi
Bork, Peer
MOCAT2: a metagenomic assembly, annotation and profiling framework
title MOCAT2: a metagenomic assembly, annotation and profiling framework
title_full MOCAT2: a metagenomic assembly, annotation and profiling framework
title_fullStr MOCAT2: a metagenomic assembly, annotation and profiling framework
title_full_unstemmed MOCAT2: a metagenomic assembly, annotation and profiling framework
title_short MOCAT2: a metagenomic assembly, annotation and profiling framework
title_sort mocat2: a metagenomic assembly, annotation and profiling framework
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978931/
https://www.ncbi.nlm.nih.gov/pubmed/27153620
http://dx.doi.org/10.1093/bioinformatics/btw183
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