SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.

The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

• Getting Started
  • Using GitHub release binaries on Linux
  • Running
• Building from sources
• User Manual
• Taxonomies
• Citation
• Contributors
• Support

SortMeRNA 4 can be run/built on Linux, and Windows (Mac coming soon).

Visit Sortmerna GitHub Releases

Linux distribution is a Shell script with the embedded installation archive.

Issue the following bash commands:

pushd ~

# get the distro
wget https://github.com/biocore/sortmerna/releases/download/v4.0.0/sortmerna-4.0.0-linux.sh

# view the installer usage
bash sortmerna-4.0.0-linux.sh --help
    Options: [defaults in brackets after descriptions]
      --help            print this message
      --version         print cmake installer version
      --prefix=dir      directory in which to install
      --include-subdir  include the sortmerna-4.0.0-Linux subdirectory
      --exclude-subdir  exclude the sortmerna-4.0.0-Linux subdirectory
      --skip-license    accept license

# run the installer
bash sortmerna-4.0.0-Linux.sh --skip-license
  sortmerna Installer Version: 4.0.0, Copyright (c) Clarity Genomics
  This is a self-extracting archive.
  The archive will be extracted to: $HOME/sortmerna
  
  Using target directory: /home/biocodz/sortmerna
  Extracting, please wait...
  
  Unpacking finished successfully

# check the installed binaries
ls -lrt /home/biocodz/sortmerna/bin/
sortmerna

# set PATH
export PATH=$HOME/sortmerna/bin:$PATH

# test the installation
sortmerna --version
SortMeRNA version 4.0.0
Build Date: Dec 11 2019
sortmerna_build_git_sha:@bc47297ce3e8580ef32d161255bfcbe1f718c322@
sortmerna_build_git_date:@2019/01/11 12:35:39@

# view help
sortmerna -h

• The only required options are --ref and --reads
• Options (any) can be specified usig a single dash e.g. -ref and -reads
• Both plain fasta/fastq and archived fasta.gz/fastq.gz files are accepted
• Relative paths are accepted

for example

# single reference and single reads file
sortmerna --ref REF_PATH --reads READS_PATH

# for multiple references use multiple '--ref'
sortmerna --ref REF_PATH_1 --ref REF_PATH_2 --ref REF_PATH_3 --reads READS_PATH

# for paired reads use '--reads' twice
sortmerna --ref REF_PATH_1 --ref REF_PATH_2 --ref REF_PATH_3 --reads READS_PATH_1 --reads READS_PATH_2

More examples can be found in test.jinja.yaml and run.py

Refer to the Manual for usage details

Build instructions

See Sortmerna Wiki - User Manual.

In case you need PDF, any modern browser can print web pages to PDF.

The folder data/rRNA_databases/silva_ids_acc_tax.tar.gz contains SILVA taxonomy strings (extracted from XML file generated by ARB) for each of the reference sequences in the representative databases. The format of the files is three tab-separated columns, the first being the reference sequence ID, the second being the accession number and the final column is the taxonomy.

If you use SortMeRNA, please cite: Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.

See AUTHORS for a list of contributors to this project.

For questions and comments, please use the SortMeRNA forum.