#### IMP3 #### 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 `German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig `_. .. toctree:: :maxdepth: 1 :caption: Installation :hidden: :name: installation installation/installation .. toctree:: :maxdepth: 1 :caption: IMP3 :hidden: :name: IMP3 running/run_idx steps/Overview output/Overview .. toctree:: :maxdepth: 1 :caption: Multi-IMP3 :hidden: :name: running_multiIMP3 multi_running/run_idx multi_steps/Overview multi_output/Overview .. toctree:: :maxdepth: 1 :caption: FAQ :hidden: :name: FAQ FAQ .. * :ref:`genindex` .. * :ref:`modindex` .. * :ref:`search`