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.