PSL-GWAS DocumentationΒΆ
PSL-GWAS performs genome-wide association studies (GWAS) on microbes using Probabilistic Soft Logic (PSL), a statistical relational programming framework.
A microbial genome-wide association study is a method for finding genetic elements associated with one or more phenotypes of interest. Genetic elements include chromosomal and plasmid genes, SNPs, indels, and copy number variants. Phenotypes of interest could include antibiotic resistance or virulence.
Given some microbial samples, including their sequenced genomes and information on which samples display which phenotypes, PSL-GWAS finds genetic elements likely to cause those phenotypes.
Unlike other microbial GWAS programs, PSL-GWAS implicitly models bacterial population structure and other domain-specific attributes, and can efficiently jointly infer over multiple phenotypes. PSL-GWAS is also easy to customize, allowing users to incorporate domain-specific knowledge in their models.
PSL-GWAS is open source and licensed under the MIT license. The source code is available on Github.