Salmon

Overview

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.

Restrictions on use

None (GPLv3+ licensed.)

Set up procedure

To access the software you must first load the modulefile:

module add apps/gcc/salmon/0.8.2

Running the application

Salmon is multi-threaded, so should be run in the smp.pe parallel environment. See the documentation concerning the appropriate number of threads to use (i.e. slots to request).

Further Information

Salmon web site