Welcome to Biohansel’s Read the Docs!¶
Currently debating on changing Subtype to Genotype in all outputs and as such, they are synonymous for biohansel in the current version (2.4.0) and in this manual
Biohansel genotypes clonal microbial whole-genome sequencing (WGS) data using SNV targeting k-mer genotyping schemes.
This tool works on genome assemblies (FASTA files) or reads (FASTQ files)! Accepts Gzipped FASTA/FASTQ files as input!
Biohansel includes 33 base-pair k-mer SNV genotyping schemes focused on Salmonella enterica subsp. enterica serovars. K-mers can be any length as long as they are a odd number.
Currently, there are subtyping schemes for the following Salmonella serovars:
- Typhi scheme adapted from Wong et al paper titled: “An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid”.
These genotyping schemes have been created, maintained, and/or adapted by Genevieve Labbe et al.
There is also an included Mycobacterium tuberculosis scheme that was modified from the Francesc Coll et al. paper titled: “A robust SNP barcode for typing Mycobacterium tuberculosis complex strains” for biohansel use by Daniel Kein.
Code is available on GitHub under https://github.com/phac-nml/biohansel.
- Genotyping Schemes
- Degenerate Base Expansion
- Galaxy Parameters