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

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 in...

Full description

Autores:
Narayanasamy, S.
Jarosz, Y.
Muller, E.E.L.
Heintz-Buschart, A.
Herold, M.
Kaysen, A.
Laczny, C.C.
Pinel, N.
May, P.
Wilmes, P.
Tipo de recurso:
Fecha de publicación:
2016
Institución:
Universidad EAFIT
Repositorio:
Repositorio EAFIT
Idioma:
eng
OAI Identifier:
oai:repository.eafit.edu.co:10784/26733
Acceso en línea:
https://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=6197
http://hdl.handle.net/10784/26733
Palabra clave:
Multi-omics
data
integration
Metagenomics
Metatranscriptomics
Microbial
ecology
Microbiome
Reproducibility
Rights
License
https://v2.sherpa.ac.uk/id/publication/issn/1474-760X
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oai_identifier_str oai:repository.eafit.edu.co:10784/26733
network_acronym_str REPOEAFIT2
network_name_str Repositorio EAFIT
repository_id_str
spelling 2021-03-23T19:52:07Z2016-12-162021-03-23T19:52:07Zhttps://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=61971474760X14747596WOS;000390200300001PUBMED;27986083SCOPUS;2-s2.0-85006345107http://hdl.handle.net/10784/2673310.1186/s13059-016-1116-8Existing 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).application/pdfengBioMed Central Ltd.https://www.scopus.com/inward/record.uri?eid=2-s2.0-85006345107&doi=10.1186%2fs13059-016-1116-8&partnerID=40&md5=d5849164661d98cf710de28113742307https://v2.sherpa.ac.uk/id/publication/issn/1474-760XAcceso abiertohttp://purl.org/coar/access_right/c_abf2GENOME BIOLOGYMulti-omicsdataintegrationMetagenomicsMetatranscriptomicsMicrobialecologyMicrobiomeReproducibilityIMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analysespublishedVersioninfo:eu-repo/semantics/publishedVersionarticleinfo:eu-repo/semantics/articleArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1Universidad EAFIT. Departamento de CienciasNarayanasamy, S.Jarosz, Y.Muller, E.E.L.Heintz-Buschart, A.Herold, M.Kaysen, A.Laczny, C.C.Pinel, N.May, P.Wilmes, P.Biodiversidad, Evolución y ConservaciónGENOME BIOLOGYORIGINALs13059-016-1116-8.pdfs13059-016-1116-8.pdfTexto completoapplication/pdf2319226https://repository.eafit.edu.co/bitstreams/f3ecf706-77ef-472c-92cc-8dfd1f2e3cf0/download36a8129b6c9130176775c698fc960827MD5110784/26733oai:repository.eafit.edu.co:10784/267332022-04-27 15:49:57.566open.accesshttps://repository.eafit.edu.coRepositorio Institucional Universidad EAFITrepositorio@eafit.edu.co
dc.title.eng.fl_str_mv IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
title IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
spellingShingle IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Multi-omics
data
integration
Metagenomics
Metatranscriptomics
Microbial
ecology
Microbiome
Reproducibility
title_short IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
title_full IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
title_fullStr IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
title_full_unstemmed IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
title_sort IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
dc.creator.fl_str_mv Narayanasamy, S.
Jarosz, Y.
Muller, E.E.L.
Heintz-Buschart, A.
Herold, M.
Kaysen, A.
Laczny, C.C.
Pinel, N.
May, P.
Wilmes, P.
dc.contributor.department.spa.fl_str_mv Universidad EAFIT. Departamento de Ciencias
dc.contributor.author.none.fl_str_mv Narayanasamy, S.
Jarosz, Y.
Muller, E.E.L.
Heintz-Buschart, A.
Herold, M.
Kaysen, A.
Laczny, C.C.
Pinel, N.
May, P.
Wilmes, P.
dc.contributor.researchgroup.spa.fl_str_mv Biodiversidad, Evolución y Conservación
dc.subject.eng.fl_str_mv Multi-omics
data
integration
Metagenomics
Metatranscriptomics
Microbial
ecology
Microbiome
Reproducibility
topic Multi-omics
data
integration
Metagenomics
Metatranscriptomics
Microbial
ecology
Microbiome
Reproducibility
description 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).
publishDate 2016
dc.date.issued.none.fl_str_mv 2016-12-16
dc.date.available.none.fl_str_mv 2021-03-23T19:52:07Z
dc.date.accessioned.none.fl_str_mv 2021-03-23T19:52:07Z
dc.type.eng.fl_str_mv publishedVersion
info:eu-repo/semantics/publishedVersion
article
info:eu-repo/semantics/article
dc.type.coarversion.fl_str_mv http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_6501
http://purl.org/coar/resource_type/c_2df8fbb1
dc.type.local.spa.fl_str_mv Artículo
status_str publishedVersion
dc.identifier.none.fl_str_mv https://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=6197
dc.identifier.issn.none.fl_str_mv 1474760X
14747596
dc.identifier.other.none.fl_str_mv WOS;000390200300001
PUBMED;27986083
SCOPUS;2-s2.0-85006345107
dc.identifier.uri.none.fl_str_mv http://hdl.handle.net/10784/26733
dc.identifier.doi.none.fl_str_mv 10.1186/s13059-016-1116-8
url https://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=6197
http://hdl.handle.net/10784/26733
identifier_str_mv 1474760X
14747596
WOS;000390200300001
PUBMED;27986083
SCOPUS;2-s2.0-85006345107
10.1186/s13059-016-1116-8
dc.language.iso.eng.fl_str_mv eng
language eng
dc.relation.uri.none.fl_str_mv https://www.scopus.com/inward/record.uri?eid=2-s2.0-85006345107&doi=10.1186%2fs13059-016-1116-8&partnerID=40&md5=d5849164661d98cf710de28113742307
dc.rights.none.fl_str_mv https://v2.sherpa.ac.uk/id/publication/issn/1474-760X
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_abf2
dc.rights.local.spa.fl_str_mv Acceso abierto
rights_invalid_str_mv https://v2.sherpa.ac.uk/id/publication/issn/1474-760X
Acceso abierto
http://purl.org/coar/access_right/c_abf2
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central Ltd.
publisher.none.fl_str_mv BioMed Central Ltd.
dc.source.none.fl_str_mv GENOME BIOLOGY
institution Universidad EAFIT
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bitstream.checksum.fl_str_mv 36a8129b6c9130176775c698fc960827
bitstream.checksumAlgorithm.fl_str_mv MD5
repository.name.fl_str_mv Repositorio Institucional Universidad EAFIT
repository.mail.fl_str_mv repositorio@eafit.edu.co
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