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.
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 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 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 denovo_map.pl 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.)
- Stacks home page
- Setting up a stacks server in cPouta