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Salmon is a tool for transcript quantification from RNA-seq data.

Salmon is available as a module on Apocrita.


To run the default installed version of Salmon, simply load the salmon module:

$ module load salmon
$ salmon --help

Usage:  salmon -h|--help or
        salmon -v|--version or
        salmon -c|--cite or
        salmon [--no-version-check] <COMMAND> [-h | options]

     index Create a salmon index
     quant Quantify a sample
     alevin single cell analysis
     swim  Perform super-secret operation
     quantmerge Merge multiple quantifications into a single file

Number of threads

By default, Salmon will run multi-threaded on all available cores. To prevent overloading a compute node, you should override this by passing the p / --threads parameter with the value of ${NSLOTS}.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load salmon

salmon index -t transcripts.fasta \
             -i transcripts_index \
             -p ${NSLOTS}

salmon quant -i transcripts_index \
             -l A \
             -1 file1.fastq \
             -2 file2.fastq \
             --validateMappings \
             -o transcripts_quant \
             -p ${NSLOTS}