Salmon 2016

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Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference.

Installed versions

Salmon is installed on the environment hpc-env/6.4 in the following versions:

  • Salmon/0.11.2-intel-2018a-Python-2.7.14
  • Salmon/0.11.3-foss-2017b-Python-2.7.14

... and on hpc-env/8.3:

  • Salmon/1.3.0-gompi-2019b

Using Salmon on the HPC cluster

To use Salmon, you have to load the corresponding environment first and then load the desired version:

module load hpc-env/6.4
module-load Salmon/0.11.2-intel-2018a-Python-2.7.14


If you want a short introduction to the available commands, you can use the help function after loading the module. Just type in:

salmon --help

The full documentation of Salmon can be found here.