Section: New Software and Platforms

SortMeRNA

Keywords: Bioinformatics - NGS - Genomic sequence

Scientific Description

SortMeRNA is a biological sequence analysis tool for metatranscriptomic and metagenomic data filtering, mapping and OTU-picking. The main application of SortMeRNA is filtering and mapping ribosomal RNA from NGS reads.

Functional Description The core algorithm is based on approximate seeds as well as an optimized text index data structure. It allows for fast and sensitive analyses of nucleotide sequences.

SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. It is implemented in C++.

• Participants: Hélène Touzet, Laurent Noé and Evguenia Kopylova

• Contact: Hélène Touzet

• URL: http://bioinfo.lille.inria.fr/RNA/sortmerna/