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IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses

Shaman Narayanasamy, Yohan Jarosz, Emilie E.L. Muller, Cédric C. Laczny, Malte Herold, Anne Kaysen, Anna Heintz-Buschart, Nicolás Pinel, Patrick May, Paul Wilmes
doi: https://doi.org/10.1101/039263
Shaman Narayanasamy
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Yohan Jarosz
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Emilie E.L. Muller
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Cédric C. Laczny
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Malte Herold
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Anne Kaysen
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Anna Heintz-Buschart
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Nicolás Pinel
2Institute of Systems Biology, 401 Terry Avenue North, WA 98109, Seattle, USA.
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Patrick May
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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Paul Wilmes
1Luxembourg Centre for Systems Biomedicine, 6 avenue du Swing, University of Luxembourg, L-4367 Belvaux, Luxembourg
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  • For correspondence: paul.wilmes@uni.lu
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Abstract

We present IMP, an automated pipeline for reproducible integrated analyses of coupled metagenomic and metatranscriptomic data. IMP incorporates preprocessing, iterative co-assembly of metagenomic and metatranscriptomic data, analyses of microbial community structure and function as well as genomic signature-based visualizations. Complementary use of metagenomic and metatranscriptomic data improves assembly quality and enables the estimation of both population abundance and community activity while allowing the recovery and analysis of potentially important components, such as RNA viruses. IMP is containerized using Docker which ensures reproducibility. IMP is available at http://r3lab.uni.lu/web/imp/.

  • Abbreviations

    NGS
    next-generation sequencing
    Contigs
    contiguous sequence(s)
    cDNA
    complementary-DNA
    MG
    Metagenomic
    MT
    Metatranscriptomic
    MP
    Metaproteome/metaproteomic
    SNPs
    single nucleotide polymorphisms
    INDELs
    insertions and deletions
    rRNA
    ribosomal RNA
    IMP
    Integrated Meta-omic Pipeline
    SM
    Simulated mock
    HF
    Human fecal
    WW
    Wastewater
    bp
    base pair
    Kb
    kilo base
    KEGG
    Kyoto Encyclopedia of Genes and Genomes
    VCF
    Variant call format
    SRA
    Sequence read archive
    NCBI
    National Center for Biotechnology Information
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    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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    Posted February 10, 2016.
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    IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses
    Shaman Narayanasamy, Yohan Jarosz, Emilie E.L. Muller, Cédric C. Laczny, Malte Herold, Anne Kaysen, Anna Heintz-Buschart, Nicolás Pinel, Patrick May, Paul Wilmes
    bioRxiv 039263; doi: https://doi.org/10.1101/039263
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    IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses
    Shaman Narayanasamy, Yohan Jarosz, Emilie E.L. Muller, Cédric C. Laczny, Malte Herold, Anne Kaysen, Anna Heintz-Buschart, Nicolás Pinel, Patrick May, Paul Wilmes
    bioRxiv 039263; doi: https://doi.org/10.1101/039263

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