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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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Covid19 #140

Closed jrober84 closed 3 years ago

jrober84 commented 3 years ago

This update is to make some minor modifications to BioHansel to be more compatible with amplicon based SARS-COV-2 data by introducing the min-kmer-frac parameter which works in combination with the min-kmer-cov parameter to ignore k-mers present in a sample which are less than the defined percentage set by the program with a default of 0.05. Additionally, the max-kmer-cov has been increased to not cause conflicts with high covered regions being ignored. The kmer report has also removed the error message field since this adds a lot of extra repeated data for these reports which adds up for larger sample pools.

github-actions[bot] commented 3 years ago

Hi @jrober84, It looks like this pull-request is has been made against the phac-nml/biohansel master branch. The master branch on repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the phac-nml/biohansel development branch. You do not need to close this PR, you can change the target branch to development by clicking the "Edit" button at the top of this page. Thanks again for your contribution!