Salmon 2016
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Introduction
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
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
Documentation
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.
