biohansel
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phac-nml
Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
It's not clear why this threshold was implemented and what kinds of situations it's supposed to be help with. It seems like it would accidentally exclude certain kmers from subtype...
Would it be possible to generate an additional output for troubleshooting that is a list of tiles where there were no positive or negative matches for each sample?
More user friendly metagenomic results
It would be great to have the option to have all internal schemes run on a sample either through the existing interface of --scheme all or another flag. BioHansel would...
Important for troubleshooting
There is currently no lower limit to k-mer length, and this could cause issues if the k-mer length is, say, below 6-10 bases, and the k-mer is found hundreds or...
Schemes should be decoupled from the codebase and put into a separate biohansel schemes public repo with version control. It would make it easier to add/update new schemes without having...
To help make it more clear what's being changed or added for the scheme creation module, it would be a good idea to have a base branch to merge into...
We want to use Biohansel pipeline in IRIDA for Campy and more species. Is it possible to include schema for Campy?
