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.

Availability

Appliacation is available for all MetaCentrum users. Versions:

  • 1.0 in module faststructure-1.0


Use

Steps to run the application

module add faststructure-1.0
structure.py

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/

Licence

The MIT License (MIT)

Program administrator

meta@cesnet.cz

Homepage

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