####WG-FAST#### The whole genome focused array SNP typing (WG-FAST) pipeline written by: Jason Sahl Email: jasonsahl at gmail dot com
for a more comprehensive overview, look at the Manual
####overview#### The goal of WG-FAST is to phylogenetically genotype an unknown sample in the context of a well studied pathogen. This sample can either be a metagenomics dataset, a metatranscriptomics dataset, or a single isolate sequencing dataset
####Installation####
- To install, enter the wgfast directory and type the command below. If you don't have sudo privileges, install to base directory using --prefix: sudo python setup.py install
- Open the script (wgfast.py) with a text editor and change the path to your WG-FAST installation directory. For example: WGFAST_PATH="/Users/jsahl/wgfast"
- To verify your installation, enter the wgfast directory and type the command below. If everything is working correctly, all tests should pass: python tests/test_all_functions.py