Pyrad

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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:

highlights

  • 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
  • The second stage editing the raw reads and is done via:
pyRAD -p params.txt -s 2