READemption 2: Multi-species RNA-Seq made easy

Abstract

Dual or Multi RNA-seq simultaneously analyze the transcriptomes of two or more interacting species to gain insights about their interplay. The RNA of the interacting species is collected and sequenced together and only separated in silico by mapping the reads to the corresponding genomes. We developed READemption 2.0, to our knowledge the first tool that performs all necessary steps to handle RNA-seq data from any number of species. These steps comprise basic quality filtering and adapter trimming of raw reads, aligning the reads to reference genomes, generating nucleotide-wise coverage files, creating gene-wise read counts and performing differential gene expression analysis. These results can be visualized by additional subcommands of the software. READemption 2.0 allows users to produce meaningful results with default settings that follow conventional standards. Furthermore, many parameters can be adjusted to meet the users specific needs, e.g. keeping or discarding species cross-mapped reads or normalizing the data.