IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Por:
Narayanasamy, S., Jarosz, Y., Muller, E.E.L., Heintz-Buschart, A., Herold, M., Kaysen, A., Laczny, C.C., Pinel, N., May, P., Wilmes, P.
Publicada:
16 dic 2016
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).
Filiaciones:
Narayanasamy, S.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Jarosz, Y.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Muller, E.E.L.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Université de Strasbourg, Present address: Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Strasbourg, France
Heintz-Buschart, A.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Herold, M.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Kaysen, A.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Laczny, C.C.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Present address: Saarland University, Building E2 1, Saarbrücken, Germany
Pinel, N.:
Institute of Systems Biology, 401 Terry Avenue North, Seattle, WA, United States
Present address: Universidad EAFIT, Carrera 49 No 7 sur 50, Medellín, Colombia
May, P.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Wilmes, P.:
Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg
Green Published, Green Submitted, gold, Gold, Green
|