The Integrated Meta-Omics Pipeline, IMP, is a reproducible and modular pipeline for large-scale integrated analysis of coupled metagenomic and metatranscriptomic data. IMP3 incorporates read preprocessing, assembly (including optional iterative co-assembly of metagenomic and metatranscriptomic data), analysis of microbial community structure (taxonomy) and function (gene functions and abundances), binning, as well as summaries and visualizations.

IMP3 is implemented in Snakemake. It is user-friendly and can be easily configured to perform single-omic metagenomic or metatranscriptomic analyses, as well as single modules, e.g. only assembly or only binning.

IMP3 is being developed at the Luxembourg Centre for Systems Biomedicine and the Swammerdam Institute for Life Sciences at the University of Amsterdam.