Reference : IMP: a pipeline for reproducible referenceindependent integrated metagenomic and meta...

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Biotechnology Life sciences : Environmental sciences & ecology Life sciences : Microbiology Life sciences : Multidisciplinary, general & others
	Focus Areas :	Systems Biomedicine
	To cite this reference:	http://hdl.handle.net/10993/30495

Title :	IMP: a pipeline for reproducible referenceindependent integrated metagenomic and metatranscriptomic analyses
Language :	English
Author, co-author :	Narayanasamy, Shaman [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Jarosz, Yohan [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Muller, Emilie [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Buschart, Anna [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Herold, Malte [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Kaysen, Anne [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Laczny, Cedric Christian [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Pinel, Nicolás [> >]
	May, Patrick [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Wilmes, Paul [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Publication date :	Dec-2016
Journal title :	Genome Biology
Publisher :	BioMed Central
Volume :	17
Pages :	260
Peer reviewed :	Yes (verified by ORBilu)
Audience :	International
ISSN :	1474-7596
e-ISSN :	1474-760X
City :	London
Country :	United Kingdom
Keywords :	[en] Multi-omics data integration ; Metagenomics ; Metatranscriptomics ; Microbial ecology ; Microbiome ; Reproducibility ; High-throughput
Abstract :	[en] Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).
Research centres :	Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group)
Funders :	Fonds National de la Recherche - FnR
Target :	Researchers ; Students ; General public ; Others
Permalink :	http://hdl.handle.net/10993/30495
DOI :	10.1186/s13059-016-1116-8
Other URL :	http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1116-8
FnR project :	FnR ; FNR3951311 > Paul Wilmes > SYSBIONAMA > Systems Biology of Natural Microbial Assemblages > 01/02/2010 > 31/01/2015 > 2009

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