Salmon

Overview

Salmon: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.

Using

Use the module name salmon to discover versions available and to load the application.

Multicore

The salmon application commands allow you define multiple cores within calls. See salmon -h for available commands, and then salmon <command> -h and/or its specific syntax for more information.

For example:

[salexan5@wilog01 ~]$ salmon index -h
...
  -p [ --threads ] arg (=2)     Number of threads to use during indexing.

[salexan5@wilog01 ~]$ salmon quant --help-reads
...
  -p [ --threads ] arg (=4)             The number of threads to use concurrently.