DDocent

Description

Getting into population genomics can be a daunting task for even an experienced population geneticist. dDocent’s purpose is to be a standalone laboratory protocol and analysis pipeline for double digest Restriction site Associated DNA (ddRAD) sequencing (the pipeline should also work with ezRAD). See the original ddRAD publication here. The laboratory protocol largely follows Peterson et al. (2012), but is focused down to specifically what has worked best for us in the Gold lab. dDocent was originally designed for marine fish populations, but can be customized for many different taxa with a little bit of hard work.

License

The MIT License (MIT)

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of dDocent and load default version of dDocent as

module avail dDocent/ # list available modules
module load dDocent   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail dDocent

and choose explicit version you want to use.

Documentation

https://ddocent.wordpress.com/about/

Homepage

https://ddocent.wordpress.com/
https://github.com/jpuritz/dDocent