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MetaTrans specifications


Unique identifier OMICS_14302
Name MetaTrans
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A sequence paired-end file.
Input format FASTQ
Output data An raw counts and differential expression files produced by the functional and taxonomical analyses.
Operating system Unix/Linux
Programming languages C, C++, Java, Perl, Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
GenomicRanges, IRanges, ShortRead, DESeq2, JRE, Python::NumPy, BioPython, USEARCH
Maintained Yes




No version available



  • person_outline Chaysavanh Manichanh

Publication for MetaTrans

MetaTrans citations


Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

PMCID: 5850319
PMID: 29535201
DOI: 10.1128/mBio.02061-17
call_split See protocol

[…] and sorted with samtools 0.1.19, alignments were inspected with IGV 2.3.55, and mapping was quantitated with htseq-count v.0.6.1p1. The code used is available at […]


Current Knowledge and Computational Techniques for Grapevine Meta Omics Analysis

Front Plant Sci
PMCID: 5767322
PMID: 29375610
DOI: 10.3389/fpls.2017.02241

[…] nd abundance of microbial pathways through sequencing data. The purpose of the suite is describing the metabolic potential of a microbial community and its members, establishing a functional profile. MetaTrans (Martinez et al., ) is an open-source pipeline, which analyzes the structure and function of an active microbial community in a sample. It was developed to analyze large amounts of data prod […]


TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

BMC Genomics
PMCID: 5644092
PMID: 29037173
DOI: 10.1186/s12864-017-4168-6

[…] a metatranscriptome analysis pipeline which is mostly suited for prokaryotes because of its use of the NCBI RefSeq database. COMAN [] maps metatranscriptome reads to bacterial reference genomes, and MetaTrans [] assigns a taxonomy based on prokaryotic 16S rRNA.Other studies construct pipelines for subparts of the analysis, including Goncalves et al. [] who constructed an R-based pipeline for pre- […]


Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches

Front Microbiol
PMCID: 5641341
PMID: 29067007
DOI: 10.3389/fmicb.2017.01941

[…] e microbiomes of selected Trebouxiophyceae, Chlorophyceae, and Zygnematophyceae obtained from the “Microalgae and Zygnematophyceae Collection Hamburg” (MZCH).Further, detailed and deep metagenome and metatrans criptome analyses identified shared and host-specific transcripts in microalgal microbiomes. This way, we have produced a detailed microbiome dataset for Chlorella saccharophila, Scenedesmus […]


Host Microbiome Interaction and Cancer: Potential Application in Precision Medicine

Front Physiol
PMCID: 5145879
PMID: 28018236
DOI: 10.3389/fphys.2016.00606

[…] Wilke et al., ), JCVI and Metagenomics Reports (METAREP) (Goll et al., ; Markowitz et al., ; Wilke et al., ) or MEGAN (Huson and Weber, ), MetAMOS (Treangen et al., ), MOCAT2 (Kultima et al., ), and MetaTrans (Martinez et al., ) which are software designed to simplify all metagenomics or metatranscriptomics pipeline; preprocessing, assembly, annotation and analysis.Having obtained a high quality […]


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MetaTrans institution(s)
Digestive Research Unit, Vall d’Hebron Research Institute, Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
MetaTrans funding source(s)
This study was supported by grants from the Instituto de Salud Carlos III/FEDER [CP13/00181, PI14/00764].

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