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.
Version on CSC's Servers
Taito: 1.46, 1.48, 2.0b, 2.3d
The command line tools of the Stacks pagage are installed in Taito. To set up the most recent stacks environment in Taito, run commands:
module load gcc/5.4.0 module load stacks
To load a specific version of Stacks use e.g.:
module load biokit/4.9.3 module load stacks/2.0
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 in taito-shell.csc.fi or as batch jobs. Note that in Taito-shell the maximum number of threads to be used is 4 (-T 4) while in batch jobs you can use larger values (up to 24 ). The Stacks installation in Taito 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.)