PyRAD
PyRAD is software to assemble de novo RADseq loci from restriction-site associated sequence data (RAD,ddRAD,GBS,PEddRAD,PEGBS) by Deren Eaton.[1]
Installed Version
pyRAD 3.0.5 is installed on Proteus. Use the following modulefile:
pyrad/3.0.5
It requires these modulefiles to be loaded, first:
python/2.7-current
vsearch
muscle
Usage
Please consult the official documentation for full details.[2] This is just a brief summary gleaned from following the author's tutorials.
Unlike most Linux programs, the options to define the behavior of the
pyRAD program are read from a text file named params.txt. To
generate a new params.txt file, do:
[juser@proteusa01 pyrad-tut]$ pyRAD -n
new params.txt file created
Then, modify params.txt. Each line of the file has a description of
the setting.
Number of Slots
There are two params in pyRAD which control the parallelization:
- line 7 -- N processors
- line 37 -- vsearch max threads per job
Some experimentation may need to be done to figure out what the appropriate values these should take given a particular hardware platform. See the pyRAD documentation.
Intalling Your Own Version
pyRAD is a set of Python 2.x scripts which require no compilation. They do, however, require some Python modules/packages. (See pyRAD documentation.)
pyRAD also requires VSEARCH (or USEARCH[3]) and MUSCLE.
Examples
D. Eaton has provided several tutorials on the pyRAD website.[4]
Translation of SE RAD Tutorial 3.0
Please see Job Script Example 05 pyRAD
References
[2]
[4]