RT Journal Article
SR Electronic
T1 IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 039263
DO 10.1101/039263
A1 Shaman Narayanasamy
A1 Yohan Jarosz
A1 Emilie E.L. Muller
A1 Cédric C. Laczny
A1 Malte Herold
A1 Anne Kaysen
A1 Anna Heintz-Buschart
A1 Nicolás Pinel
A1 Patrick May
A1 Paul Wilmes
YR 2016
UL http://biorxiv.org/content/early/2016/02/10/039263.abstract
AB 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/.NGSnext-generation sequencingContigscontiguous sequence(s)cDNAcomplementary-DNAMGMetagenomicMTMetatranscriptomicMPMetaproteome/metaproteomicSNPssingle nucleotide polymorphismsINDELsinsertions and deletionsrRNAribosomal RNAIMPIntegrated Meta-omic PipelineSMSimulated mockHFHuman fecalWWWastewaterbpbase pairKbkilo baseKEGGKyoto Encyclopedia of Genes and GenomesVCFVariant call formatSRASequence read archiveNCBINational Center for Biotechnology Information