Welcome to the website of the Integrated Meta-Omics Pipeline, a.k.a., IMP!
IMP is a reproducible and modular pipeline for large-scale standardized integrated analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly of metagenomic and metatranscriptomic data, analyses of microbial community structure and function as well as genomic signature-based visualizations. As an added functionality, IMP also performs either single-omic metagenomic or metatranscriptomic analyses.
Currently (version 2.0), IMP covers the following tasks:
- Preprocessing
- Assembly
- Analysis
- Binning
- Report
and we are working hard to integrate more, e.g., taxonomic profiling at different levels (gene(s) and genomes).
IMP version 1
IMP v.1 uses the Docker framework to create a container thereby enabling reproducible installation and execution. We consider this to be useful in case you have access to your own compute resources, i.e., a server where you have administration rights.
For more information on IMP v.1 please check the dedicated page.
IMP version 2
While the Docker framework provides several benefits, it requires administration rights. This, however, is not always possible, in particular in the case of HPC environments. Hence, we have ported IMP to use the conda framework instead. For details on the conda-based installation, please check the Installation page.
In addition, we are working on the implementation of additional functionality to further ease the integration of multi-omic data for microbiome research.
Cite
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. Genome Biol. 2016 Dec 16;17(1):260. Narayanasamy S, Jarosz Y, Muller EE, Heintz-Buschart A, Herold M, Kaysen A, Laczny CC, Pinel N, May P, Wilmes P. |
Please cite also the papers of the tools included in IMP!