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 a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files specified by the user. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1 (http://qiime.org). SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.
Visit http://bioinfo.lifl.fr/RNA/sortmerna/ for more information.
- Documentation
- Compilation
- Install compilers, ZLIB and autoconf
- Tests
- Third-party libraries
- Wrappers and packages
- Taxonomies
- Citation
- Contributors
If you have Doxygen installed, you can generate the documentation
by modifying the following lines in doxygen_configure.txt:
INPUT = /path/to/sortmerna/include /path/to/sortmerna/src
IMAGE_PATH = /path/to/sortmerna/algorithm
and running the following command:
doxygen doxygen_configure.txt
This command will generate a folder html in the directory from which the
command was run.
NOTE: You will require autoconf to build from the git cloned
repository or from source code in the Source code tar
balls under release Downloads.
(0) Prepare your build system for compilation:
bash autogen.sh(1) Check your GCC compiler is version 4.0 or higher:
gcc --version(2) Run configure and make scripts:
./configure
make(3) To install:
make installYou can define an alternative installation directory by
specifying --prefix=/path/to/installation/dir to configure.
(1) Check the version of your C/C++ compiler:
gcc --versionIf the compiler is LLVM-GCC (deprecated, see Deprecation and Removal Notice), then you must set it to Clang or the original GCC compiler (installable via MacPorts).
(2a) To set your compiler to Clang (check you have it "clang --version", if not then see "Install Clang for Mac OS" below):
export CC=clang
export CXX=clang++Run configure and make scripts with default parameters:
./configure
make(2b) To set your compiler to the original GCC (check you have it "gcc-mp-4.8 --version", if not then see "Install GCC through MacPorts" below):
export CC=gcc-mp-4.8
export CXX=g++-mp-4.8If using the original GCC compiler, Zlib should also be installed via MacPorts in order for compression to work (read .zip and .gz files). See section "Install GCC and Zlib though MacPorts" below for installation instructions.
Assuming you have Zlib installed:
Run configure and make scripts (if compression feature wanted):
./configure --with-zlib="/opt/local"
makeOtherwise (if compression feature not wanted):
./configure --without-zlib
make(3) To install:
make installYou can define an alternative installation directory by
specifying --prefix=/path/to/installation/dir to configure.
NOTE: the Clang compiler on Mac (distributed through Xcode) does not support multithreading. A preliminary implementation of OpenMP for Clang has been made at "http://clang-omp.github.io" though has not been yet incorporated into the Clang mainline. The user may follow the steps outlined in the above link to install the version of Clang with multithreading support, though this version has not yet been tested with SortMeRNA. Otherwise, the user is recommended to install the original GCC compiler via MacPorts (contains full multithreading support).
Installing Xcode (free through the App Store) and Xcode command line tools will automatically install the latest version of Clang supported with Xcode.
After installing Xcode, the Xcode command line tools may be installed via:
Xcode -> Preferences -> Downloads
Under "Components", click to install "Command Line Tools"
Assuming you have MacPorts installed, type:
sudo port selfupdate
sudo port install gcc48
sudo port install zlibAfter the installation, you should find the compiler installed in /opt/local/bin/gcc-mp-4.8 and /opt/local/bin/g++-mp-4.8 as well as Zlib in /opt/local/lib/libz.dylib and /opt/local/include/zlib.h .
wget http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz
tar -zxvf autoconf-2.69.tar.gz
cd autoconf-2.69
./configure
make
make installYou can define an alternative installation directory by
specifying --prefix=/path/to/installation/dir to configure
(before calling make).
If installing in a directory other than those listed in $PATH, add the installation directory to $PATH:
export PATH=$PATH:/path/to/installation/dirUsage tests can be run with the following command:
python ./tests/test_sortmerna.py
python ./tests/test_sortmerna_zlib.py
Make sure the data folder is in the same directory as test_sortmerna.py
Various features in SortMeRNA are dependent on third-party libraries, including:
- ALP: computes statistical parameters for Gumbel distribution (K and Lambda)
- CMPH: C Minimal Perfect Hashing Library
- KSEQ: FASTA/FASTQ parser (including compressed files)
- SSW: SIMD Smith-Waterman C/C++ Library
Thanks to Björn Grüning and Nicola Soranzo, an up-to-date Galaxy wrapper exists for SortMeRNA. Please visit Björn's github page for installation.
Thanks to the Debian Med team, SortMeRNA 2.0 is now a package in Debian. Thanks to Andreas Tille for the sortmerna and indexdb_rna man pages (version 2.0). These have been updated for 2.1 in the master repository.
Thanks to Ben Woodcroft for adding SortMeRNA 2.1 to GNU Guix, find the package here.
SortMeRNA 2.0 can be used in QIIME's pick_closed_reference_otus.py, pick_open_reference_otus.py and assign_taxonomy.py scripts.
Note: At the moment, only 2.0 is compatible with QIIME.
The folder 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.