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/.
Abbreviations
- NGS
- next-generation sequencing
- Contigs
- contiguous sequence(s)
- cDNA
- complementary-DNA
- MG
- Metagenomic
- MT
- Metatranscriptomic
- MP
- Metaproteome/metaproteomic
- SNPs
- single nucleotide polymorphisms
- INDELs
- insertions and deletions
- rRNA
- ribosomal RNA
- IMP
- Integrated Meta-omic Pipeline
- SM
- Simulated mock
- HF
- Human fecal
- WW
- Wastewater
- bp
- base pair
- Kb
- kilo base
- KEGG
- Kyoto Encyclopedia of Genes and Genomes
- VCF
- Variant call format
- SRA
- Sequence read archive
- NCBI
- National Center for Biotechnology Information
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Posted February 10, 2016.
IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses
