Genome BiologyBioinformaticsPeer-reviewed journal article
IMP: a pipeline for reproducible metagenomic and metatranscriptomic analyses
Shaman NarayanasamyiD, Yohan Jarosz, Emilie E.L. Muller, Cédric C. Laczny, Malte HeroldiD, Anne KayseniD, Anna Heintz-Buschart, Nicolás Pinel, Patrick MayiD, Paul WilmesiD
Abstract
We present IMP, an automated pipeline for reproducible integrated analyses of coupled metagenomic and metatranscriptomic data. IMP incorporates preprocessing, iterative co-assembly of metagenomic and metatranscriptomic data, analyses of microbial community structure and function as well as genomic signature-based visualizations. Complementary use of metagenomic and metatranscriptomic data improves assembly quality and enables the estimation of both population abundance and community activity while allowing the recovery and analysis of potentially important components, such as RNA viruses. IMP is containerized using Docker which ensures reproducibility. IMP is available at http://r3lab.uni.lu/web/imp/.
- assay: metagenomics
- research focus: clustering
- research focus: dimensionality reduction
- approach: deep learning
- approach: statistical model
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