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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.


Free to use and open source under GNU GPLv3.


Puhti: 2.54


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

module load biokit

After that you can launch Stacks commands like . for example:  -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 in 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 runs.

It is howerver possible to set up your own Stacks database and WWW interface to a virtual machine running in the cPouta cloud environment of CSC. (Link to instrctions to set up a Stacks server in cPouta can be found form the end of this page.)


Last edited Mon Mar 29 2021