Pyrad

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:

• http://nbviewer.jupyter.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD_3.0.ipynb

(note this tutorial assumes the executable is pyRAD, while in actuality, there are are only lower-case letter in the executable name).

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.
• If using a Gridengine job script, be sure to match the "-pe multi" value and number of CPUs in "params.txt" to have the same value.
• The first stage is de-multiplexing your short read dataset using the barcodes, a processes which will generate new fastq file depending on the barcodes. This is done via:

pyrad -p params.txt -s 1

• The second stage editing the raw reads for quality and is done via:

pyrad -p params.txt -s 2