MetaTrans: an open-source pipeline for metatranscriptomics of the human gut microbiome. human gut metagenome

To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline isdesigned to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, and differential gene expression analysis and also maps reads against functional databases. Its efficacy was validated with data obtained from a previous study and from sequences that we generated from eighthuman fecal samples collected before and after a flatulogenic diet challenge. Metatrans is written in the closest language to the operating system in order to be able to easily include third-party tools in each of its stages.