indexdb_rna

tool for filtering, mapping and OTU-picking NGS reads

Install

All systems
curl cmd.cat/indexdb_rna.sh
Debian Debian
apt-get install sortmerna
Ubuntu
apt-get install sortmerna
image/svg+xml Kali Linux
apt-get install sortmerna
Windows (WSL2)
sudo apt-get update sudo apt-get install sortmerna
Dockerfile
dockerfile.run/indexdb_rna

sortmerna

tool for filtering, mapping and OTU-picking NGS reads

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). 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.