FastStructure

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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/

Homepage

URL: http://rajanil.github.io/fastStructure/