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
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
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The easiest way to install is through conda:
conda create -n wgfast python=3.6
source activate wgfast
#previous required versions: gatk4=4.2.6.1, picard=2.27.4
conda install -c bioconda gatk4 picard raxml samtools bbmap dendropy minimap2 biopython
#You might need to install Bioconda with: pip install Biopython -
Download the wgfast github repository, install:
git clone https://github.com/jasonsahl/wgfast.git
python setup.py build
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