IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Fecha
2016-12-16
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.
Título de la revista
ISSN de la revista
Título del volumen
Editor
BioMed Central Ltd.
Resumen
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).