MOCAT protocols

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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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Maintainer


  • person_outline Peer Bork <>

Publications for MOCAT

MOCAT in pipelines

 (5)
2017
PMCID: 5474096
PMID: 28630803
DOI: 10.7717/peerj.3428

[…] sequencing cycles), and bases with a quality score lower than 20. lastly, a size threshold of 95 bp was imposed on the entire read dataset. reads were assembled using the soapdenovo software in the mocat pipeline. the assembled contigs were then confirmed to be viral in origin using the virsorter software with default settings (; ). the viral fraction of the etnp metagenomic dataset […]

2017
PMCID: 5648452
PMID: 29047329
DOI: 10.1186/s12864-017-4195-3

[…] 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 […]

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

[…] the manuscript, we used speci clusters at the species level related via the ncbi taxonomy database as a taxonomic reference. additionally, motu abundances were also determined using standard mocat procedures (sunagawa et al, ), but exclusively used to estimate species diversity ()., for calling genomic variants, all metagenomic sequencing reads were additionally mapped to a reference set […]

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

[…] a best-hit approach with a minimum of 98% sequence identity between matches (using usearch with default settings)., raw paired-end illumina fastq files from metagenomic samples were processed using mocat (version 1.2) (kultima et al, ), by first removing low-quality reads (option read_trim_filter with length cutoff 45 and quality cutoff 20). retained high-quality (hq) reads were screened […]

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 […]


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MOCAT in publications

 (30)
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 […]

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., ) […]

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 […]

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 […]

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 […]


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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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