SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

TLDR

Next‑generation sequencing of community RNA produces a mix of coding and non‑coding fragments, and separating ribosomal RNAs from messenger RNAs is essential for gene‑expression analysis and phylogenetic profiling. The authors introduce SortMeRNA, a new tool for rapidly filtering rRNA fragments from metatranscriptomic datasets. SortMeRNA processes large read collections, matching them against an rRNA database with high sensitivity while maintaining low runtime. The program is freely available at http://bioinfo.lifl.fr/RNA/sortmerna (contact: [e-mail]); supplementary data are provided online.

Abstract

Abstract Motivation: The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. Results: We present SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time. Availability: http://bioinfo.lifl.fr/RNA/sortmerna Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.