Difference between revisions of "Stacks"
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If you want to use Stacks on the HPC cluster, you will have to load the corresponding module. You can do that by using the command | If you want to use Stacks on the HPC cluster, you will have to load the corresponding module. You can do that by using the command | ||
module load Stacks | module load Stacks/2.1-foss-2016b | ||
if you are using the standard environment ''hpc-uniol-env''. | |||
Should you need Stack to run with the intel compiler you would have to change the environment to ''hpc-env/6.4'' and load Stack with the foss toolchain: | |||
ml hpc-env/6.4 | |||
ml Stacks/2.1-intel-2018a | |||
== Documentation == | == Documentation == | ||
A manual for Stacks can be found [http://catchenlab.life.illinois.edu/stacks/manual/ here]. | A manual for Stacks can be found [http://catchenlab.life.illinois.edu/stacks/manual/ here]. | ||
Revision as of 09:51, 24 July 2018
Introduction
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.
Installed version
The currently installed versions of Stacks are
1.42
2.1
Using Stacks on the HPC cluster
If you want to use Stacks on the HPC cluster, you will have to load the corresponding module. You can do that by using the command
module load Stacks/2.1-foss-2016b
if you are using the standard environment hpc-uniol-env.
Should you need Stack to run with the intel compiler you would have to change the environment to hpc-env/6.4 and load Stack with the foss toolchain:
ml hpc-env/6.4 ml Stacks/2.1-intel-2018a
Documentation
A manual for Stacks can be found here.
