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phac-nml / biohansel

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
Apache License 2.0
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Update needed for S. Typhi scheme #128

Closed glabbe closed 3 years ago

glabbe commented 3 years ago

There were 7 new targets added in the S. Typhi scheme since the publication of the original scheme by Wong et al (2016). These are used by the genotyphi tool (https://github.com/katholt/genotyphi). We need to update the scheme in BioHansel, as well as the metadata file and the citations for the adapted scheme. We have also performed an analysis of the WGS data and associated source metadata from ~8,100 public S. Typhi genomes which will be presented in the revised BioHansel manuscript, and need to update the metadata file with additional fields.

glabbe commented 3 years ago

Still need to update the test file (pytest) for the Typhi scheme and Typhi scheme version - now done in pull request #131

glabbe commented 3 years ago

This was addressed in pull request #131