Fast filtering, mapping and OTU picking
SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. 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 ribosomal RNA 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.
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.
SortMeRNA is implemented in C++ and freely distributed under the GNU lesser general public license (LGPL).
The latest v2.1 (2 February 2016),
- Version 2.1 source code: download
- Version 2.1 binary for Linux 64-bit: download
- Version 2.1 binary for Mac OS X 64-bit (compiled using GCC multi-threading supported): download
- Version 2.0 source code: download
- Version 2.0 binary for Linux 64-bit: download
- Version 2.0 binary for Mac OS X 64-bit (compiled using Clang, multi-threading not supported): download
- Version 2.0 binary for Mac OS X 64-bit (compiled using GCC, multi-threading supported): download
- Version 1.9 beta (11 March 2014) source code: download
- Version 1.9 beta binary Linux 64-bit (compiled using Red Hat): download
- Version 1.9 beta binary Mac OS X 64-bit (compiled on OS 10.9 using Clang): download
- Version 1.9 (30 Aug 2013) source code supporting the buildtrie executable: download
Ongoing development for v2.1 can be followed on GibHub.
To download the development version:
- clone the repository to a working directory:
git clone https://github.com/biocore/sortmerna.git
- or, download the repository as a zipped folder by clicking on the button "Download ZIP" from the main repository page
Good to Know
SortMeRNA is known to have linking problems using Apple's llvm-gcc
compiler (ex. llvm-gcc-4.2), as of Xcode 5 the llvm-gcc compiler has
deprecated (see "Deprecation and Removal Notice"). Please use either Clang or the original GCC compiler (installable from MacPorts) (see README.md for details).
Additionally, Clang does not easily support OpenMP for multithreading and thus it is strongly recommended to use the original GCC compiler (versions 4.0 and up, available through MacPorts) if multithreading is desired.
Users are encouraged to submit bug reports or issues to the SortMeRNA issue tracker on GitHub, or sending an e-mail to the authors.