IMP: a pipeline for reproducible referenceindependent 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 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).