QmihR: Pipeline for quantification of microbiome in human RNA-seq

Abstract

The huge amount of genomic and transcriptomic data obtained to characterize human diversity can also be exploited to indirectly gather information on the human microbiome. Here we present the pipeline QmihR designed to identify and quantify the abundance of known microbiome communities and to search for new/rare pathogenic species in RNA-seq datasets. We applied QmihR to 36 RNA-seq tumor tissue samples from Ukrainian gastric carcinoma patients available in TCGA, in order to characterize their microbiome and check for efficiency of the pipeline. The microbes present in the samples were in accordance to published data in other European datasets, and the independent BLAST evaluation of microbiome-aligned reads confirmed that the assigned species presented the highest BLAST match-hits. QmihR is available at GitHub (https://github.com/ Pereira-lab/QmihR).