Introduction

Software for RADseq

module load pyrad

will load the necessary software, mainly muscle and vsearch.

Guides

The go-to tutorial for this is at:

with the pyrad module loaded, the "pyrad "executable is immediately available on the command line
one of "-p", "-d", "-D" and "-n" options are essential.
"pyrad -n" generates a "params.txt" file which contains settings for the run. A large part of the analysis can be configured by editing this file.
The first stage is to gather statistics about your short read dataset and the barcodes. This is done via:

pyRAD -p params.txt -s 1

pyRAD -p params.txt -s 2