IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

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dc.citation.journalTitleGENOME BIOLOGYspa
dc.contributor.authorNarayanasamy, S.
dc.contributor.authorJarosz, Y.
dc.contributor.authorMuller, E.E.L.
dc.contributor.authorHeintz-Buschart, A.
dc.contributor.authorHerold, M.
dc.contributor.authorKaysen, A.
dc.contributor.authorLaczny, C.C.
dc.contributor.authorPinel, N.
dc.contributor.authorMay, P.
dc.contributor.authorWilmes, P.
dc.contributor.departmentUniversidad EAFIT. Departamento de Cienciasspa
dc.contributor.researchgroupCiencias Biológicas y Bioprocesos (CIBIOP)spa
dc.date.accessioned2021-03-23T20:08:59Z
dc.date.available2021-03-23T20:08:59Z
dc.date.issued2016-12-16
dc.description.abstractExisting 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).eng
dc.identifierhttps://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=6197
dc.identifier.doi10.1186/s13059-016-1116-8spa
dc.identifier.issn1474760Xspa
dc.identifier.issn14747596spa
dc.identifier.otherWOS;000404477300001
dc.identifier.otherSCOPUS;2-s2.0-85041521409
dc.identifier.urihttp://hdl.handle.net/10784/26821
dc.language.isoengeng
dc.publisherBioMed Central Ltd.
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85006345107&doi=10.1186%2fs13059-016-1116-8&partnerID=40&md5=d5849164661d98cf710de28113742307
dc.rightshttps://v2.sherpa.ac.uk/id/publication/issn/1474-760X
dc.sourceGENOME BIOLOGY
dc.subject.keywordMulti-omics data integrationeng
dc.subject.keywordMetagenomicseng
dc.subject.keywordMetatranscriptomicseng
dc.subject.keywordMicrobial ecologyeng
dc.subject.keywordMicrobiomeeng
dc.subject.keywordReproducibilityeng
dc.titleIMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyseseng
dc.typearticleeng
dc.typeinfo:eu-repo/semantics/articleeng
dc.typeinfo:eu-repo/semantics/publishedVersioneng
dc.typepublishedVersioneng
dc.type.localArtículo

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