RRAP: RPKM Recruitment Analysis Pipeline
Conner Y. Kojima, Eric W. Getz, J. Cameron Thrash
Abstract
A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools.
Topics & Concepts
BiologyMetagenomicsPipeline (software)Computational biologyGenomeGeneticsEngineeringGeneMechanical engineeringGenomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyGut microbiota and health