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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Peer Bork

Publications for MOCAT

MOCAT citations

 (31)
library_books

A Large Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom Forming Microcystis Epibiont Communities

2018
Front Microbiol
PMCID: 5919953
PMID: 29731741
DOI: 10.3389/fmicb.2018.00746

[…] the genera to which the genome bins were assigned based on both whole-genome sequences and 16s rrna genes., functional characterization and annotation of protein-encoding genes were performed by mocat2 (kultima et al., ). the protein-encoding genes of each sample were separately submitted to the automatic annotation server ghostkoala (last updated march 4, 2016) (kanehisa et al., ) […]

library_books

Comparison of normalization methods for the analysis of metagenomic gene abundance data

2018
BMC Genomics
PMCID: 5910605
PMID: 29678163
DOI: 10.1186/s12864-018-4637-6

[…] in 68 different locations across the globe []. dna was sequenced using illumina sequencing resulting in an average of 3.2·108 reads per sample. reads were mapped to an oceanic gene catalog using mocat v1.2 [] using the eggnog database v3.0. the count data was received directly from the project authors. we selected the largest homogeneous experimental condition consisting of 45 metagenomes […]

library_books

Similarity of the dog and human gut microbiomes in gene content and response to diet

2018
Microbiome
PMCID: 5907387
PMID: 29669589
DOI: 10.1186/s40168-018-0450-3

[…] ancestor of this neighborhood. this analysis was performed with the jug scripts [] in the taxonomic directory of the supplementary source code., functional annotation of genes was performed using mocat2, which was also used to generate abundance profiles []. kegg orthologous (ko) groups were filtered to include only kos which were used in the annotation of prokaryotic species (thus removing […]

library_books

Plastid Transcript Editing across Dinoflagellate Lineages Shows Lineage Specific Application but Conserved Trends

2018
Genome Biol Evol
PMCID: 5888634
PMID: 29617800
DOI: 10.1093/gbe/evy057

[…] of 13 nondinoflagellate orthologues, using the corresponding programmes in-built into the cipres gateway (; ; ), and the default conditions., available raw reads for p. lunula were filtered using mocat2 () with length and quality cut-offs of 45 and 30. filtered reads were subsequently mapped to consensus gdna sequences using bwa (), and filtered for unique mappers with at least 95% similarity […]

library_books

Subspecies in the global human gut microbiome

2017
Mol Syst Biol
PMCID: 5740502
PMID: 29242367
DOI: 10.15252/msb.20177589

[…] reads were quality‐filtered and screened against the human genome sequence for removing contamination as previously described (zeller et al, ). species abundance was calculated using established mocat (kultima et al, ) protocols for speci clusters (mende et al, ). throughout the manuscript, we used speci clusters at the species level related via the ncbi taxonomy database as a taxonomic […]

call_split

Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

2017
BMC Genomics
PMCID: 5648452
PMID: 29047329
DOI: 10.1186/s12864-017-4195-3
call_split See protocol

[…] were available in the gigascience database (http://www.gigadb.org/). metagenomic samples were basically processed (e.g. high-quality reads extraction and host dna contamination removing) using the mocat pipeline [] under the bioinformatic platforms at beijing genomics institute (bgi)-shenzhen., metagenomic reads were assembled using megahit (a de novo assembler for large and complex […]


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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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