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Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Installed version

These versions are installed and and currently available ...

... on envirnoment hpc-uniol-env:

  • Stacks/1.42
  • Stacks/2.1-foss-2016b

... on environment hpc-env/6.4:

  • Stacks/2.1-intel-2018a
  • Stacks/2.4-intel-2018a
  • Stacks/2.41-foss-2017b

... on environment hpc-env/8.3:

  • Stacks/2.57-iccifort-2019b

Using Stacks on the HPC cluster

If you want to use Stacks on the HPC cluster, you will have to load the corresponding module. If you are using the standard environment hpc-uniol-env you can do that by using the command

module load Stacks/2.1-foss-2016b

Should you need Stacks to run with the intel compiler you would have to change the environment to hpc-env/6.4 and load Stack with the intel toolchain:

ml hpc-env/6.4
ml Stacks/2.1-intel-2018a


A manual for Stacks can be found here.