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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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IRIDA-Biohansel: Adding our own schema for other Species #126

Open ajkarloss opened 3 years ago

ajkarloss commented 3 years ago

We want to use Biohansel pipeline in IRIDA for Campy and more species. Is it possible to include schema for Campy?

glabbe commented 3 years ago

Campy has high genetic diversity, so a cgMLST approach may be better than a SNP-based approach for this pathogen. That said, we are currently developing an automated schema-production tool, and we will explore its usefulness with more genetically diverse pathogens, such as Campy. We will include links and information on the BioHansel GitHub page as new schemas and tools are available. Thank you for the suggestion @ajkarloss

ajkarloss commented 3 years ago

What about Listeria?

glabbe commented 3 years ago

@ajkarloss we have started a project to create subtyping schemas for some of the major clonal complexes of Listeria (CC1, CC2, and CC4). We however expect to determine the clonal complex using MLST, prior to running these BioHansel schemas.