A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets.

ABSTRACT:

Background

Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy.

Results

The metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenet

SUBMITTER: Leimena MM 

PROVIDER: S-EPMC3750648 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature