Salmon

Description

Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run Salmon is a FASTA file containing your reference transcripts and a (set of) FASTA/FASTQ file(s) containing your reads. Optionally, Salmon can make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads.

License

GNU General Public License

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of salmon and load default version of salmon as

module avail salmon/ # list available modules
module load salmon   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail salmon

and choose explicit version you want to use.

Documentation

http://salmon.readthedocs.io/en/latest/salmon.html

Homepage

http://salmon.readthedocs.io/en/latest/index.html https://github.com/COMBINE-lab/salmon