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

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dc.citation.journalTitleGENOME BIOLOGY
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.researchgroupBiodiversidad, Evolución y Conservaciónspa
dc.date.accessioned2021-03-23T19:52:07Z
dc.date.available2021-03-23T19:52:07Z
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.formatapplication/pdf
dc.identifierhttps://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=6197
dc.identifier.doi10.1186/s13059-016-1116-8
dc.identifier.issn1474760X
dc.identifier.issn14747596
dc.identifier.otherWOS;000390200300001
dc.identifier.otherPUBMED;27986083
dc.identifier.otherSCOPUS;2-s2.0-85006345107
dc.identifier.urihttp://hdl.handle.net/10784/26733
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.rights.accessrightsinfo:eu-repo/semantics/openAccesseng
dc.rights.localAcceso abiertospa
dc.sourceGENOME BIOLOGY
dc.subjectMulti-omicseng
dc.subjectdataeng
dc.subjectintegrationeng
dc.subjectMetagenomicseng
dc.subjectMetatranscriptomicseng
dc.subjectMicrobialeng
dc.subjectecologyeng
dc.subjectMicrobiomeeng
dc.subjectReproducibilityeng
dc.titleIMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyseseng
dc.typepublishedVersioneng
dc.typeinfo:eu-repo/semantics/publishedVersioneng
dc.typearticleeng
dc.typeinfo:eu-repo/semantics/articleeng
dc.type.localArtículospa

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