IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
dc.citation.journalTitle | GENOME BIOLOGY | |
dc.contributor.author | Narayanasamy, S. | |
dc.contributor.author | Jarosz, Y. | |
dc.contributor.author | Muller, E.E.L. | |
dc.contributor.author | Heintz-Buschart, A. | |
dc.contributor.author | Herold, M. | |
dc.contributor.author | Kaysen, A. | |
dc.contributor.author | Laczny, C.C. | |
dc.contributor.author | Pinel, N. | |
dc.contributor.author | May, P. | |
dc.contributor.author | Wilmes, P. | |
dc.contributor.department | Universidad EAFIT. Departamento de Ciencias | spa |
dc.contributor.researchgroup | Biodiversidad, Evolución y Conservación | spa |
dc.date.accessioned | 2021-03-23T19:52:07Z | |
dc.date.available | 2021-03-23T19:52:07Z | |
dc.date.issued | 2016-12-16 | |
dc.description.abstract | 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). | eng |
dc.format | application/pdf | |
dc.identifier | https://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=6197 | |
dc.identifier.doi | 10.1186/s13059-016-1116-8 | |
dc.identifier.issn | 1474760X | |
dc.identifier.issn | 14747596 | |
dc.identifier.other | WOS;000390200300001 | |
dc.identifier.other | PUBMED;27986083 | |
dc.identifier.other | SCOPUS;2-s2.0-85006345107 | |
dc.identifier.uri | http://hdl.handle.net/10784/26733 | |
dc.language.iso | eng | eng |
dc.publisher | BioMed Central Ltd. | |
dc.relation.uri | 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 | https://v2.sherpa.ac.uk/id/publication/issn/1474-760X | |
dc.rights.accessrights | info:eu-repo/semantics/openAccess | eng |
dc.rights.local | Acceso abierto | spa |
dc.source | GENOME BIOLOGY | |
dc.subject | Multi-omics | eng |
dc.subject | data | eng |
dc.subject | integration | eng |
dc.subject | Metagenomics | eng |
dc.subject | Metatranscriptomics | eng |
dc.subject | Microbial | eng |
dc.subject | ecology | eng |
dc.subject | Microbiome | eng |
dc.subject | Reproducibility | eng |
dc.title | IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses | eng |
dc.type | publishedVersion | eng |
dc.type | info:eu-repo/semantics/publishedVersion | eng |
dc.type | article | eng |
dc.type | info:eu-repo/semantics/article | eng |
dc.type.local | Artículo | spa |
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