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Warning!

Puhti and Mahti will be decommissioned after Roihu becomes available. Users should clean up unnecessary files and move any required data by the end of August 2026. See the Roihu data preparation instructions for details.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

Stacks

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.

License

Free to use and open source under GNU GPLv3.

Available

  • Puhti: 2.62, 2.65

Usage

The command-line tools of the Stacks package are installed on Puhti. To set up the most recent stacks environment on Puhti, run the command:

module load biokit

After that you can launch Stacks commands like denovo_map.pl. For example:

denovo_map.pl -m 3 -M 2 -n 3 -T 4 -S -b 1 -t -a 2010-11-30 -o ./stacks -p ./samples/male.fa -p ./samples/female.fa -r ./samples/progeny_1.fa -r ./samples/progeny_2.fa -r ./samples/progeny_3.fa

As stacks jobs can be rather heavy, they should be executed as batch jobs. The Stacks installation on Puhti is not linked to a stacks result database and web interface. Because of that you should use option -S (and not options -B and -D) in denovo_map.pl runs.

It is, however, possible to set up your own Stacks database and WWW interface to a virtual machine running in the cPouta cloud environment of CSC. See more details here.

More information