MOCAT pipeline

MOCAT specifications

Information


Unique identifier OMICS_01517
Name MOCAT
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Single- and paired-end reads
Input format FastQ
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Peer Bork <>

Publications for MOCAT

MOCAT IN pipelines

 (2)
2015
PMCID: 4681832
PMID: 26734060
DOI: 10.3389/fgene.2015.00348

[…] phylogenetic marker. therefore, in whole metagenome shotgun sequencing, we can use software to search single copy marker genes in other databases. two examples of programs using these approaches are mocat (kultima et al., 2012), which uses the refmg database (ciccarelli et al., 2006) constituted by a collection of 40 single copy marker genes, and amphora (wu and eisen, 2008), which includes […]

2014
PMCID: 4299606
PMID: 25432777
DOI: 10.15252/msb.20145645

[…] the metagenomic gene catalog (see above) with the profile hmm for each toxin and quantified the abundance of matching sequences in participants of study population f (using the above-described mocat routines). statistical significance was established using the wilcoxon test (supplementary table s2)., the shotgun metagenomic sequencing data and the 16s rrna amplicon sequencing data […]

MOCAT institution(s)
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany; Max Delbrück Centre for Molecular Medicine, Berlin, Germany
MOCAT funding source(s)
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].

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