FastStructure
Description
FastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm on a test simulated genotype dataset.
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 faststructure and load default version of faststructure as
module avail faststructure/ # list available modules module load faststructure # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail faststructure
and choose explicit version you want to use.
The application can be run by command python structure.py according to the official fastStructure manual. In MataCentrum you can run it only by structure.py, because we made the file runnable. If you would like to use original syntax, you should type whole path to the file (python /software/faststructure/1.0/structure.py).
Documentation
Documentation can be found at http://rajanil.github.io/fastStructure/