title: IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.
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).
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.
authors.forename: Shaman
authors.initials: S
authors.lastname: Narayanasamy
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.
authors.forename: Yohan
authors.initials: Y
authors.lastname: Jarosz
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.|Present address: Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France.
authors.forename: Emilie E L
authors.initials: EE
authors.lastname: Muller
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.
authors.forename: Anna
authors.initials: A
authors.lastname: Heintz-Buschart
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.
authors.forename: Malte
authors.initials: M
authors.lastname: Herold
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.
authors.forename: Anne
authors.initials: A
authors.lastname: Kaysen
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.|Present address: Saarland University, Building E2 1, Saarbrücken, 66123, Germany.
authors.forename: Cédric C
authors.initials: CC
authors.lastname: Laczny
authors.affiliation: Institute of Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA.|Present address: Universidad EAFIT, Carrera 49 No 7 sur 50, Medellín, Colombia.
authors.forename: Nicolás
authors.initials: N
authors.lastname: Pinel
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg.
authors.forename: Patrick
authors.initials: P
authors.lastname: May
authors.affiliation: Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette, L-4362, Luxembourg. paul.wilmes@uni.lu.
authors.forename: Paul
authors.initials: P
authors.lastname: Wilmes
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D023281:Genomics; D054892:Metagenome / Q000235:genetics*; D064307:Microbiota / Q000235:genetics*; D012984:Software; D059467:Transcriptome / Q000235:genetics*; D057188:Workflow
keywords: Metagenomics; Metatranscriptomics; Microbial ecology; Microbiome; Multi-omics data integration; Reproducibility