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dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.
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update charcoal with functions from `sourmash.tax` #204

Open ctb opened 2 years ago

ctb commented 2 years ago

With the merge of https://github.com/sourmash-bio/sourmash/pull/1543 and https://github.com/sourmash-bio/sourmash/pull/1651, among others, we have a lot of ~duplicated functionality between charcoal and sourmash. We should change charcoal over to using sourmash functions where possible, just as we did with sourmash.lca.lca_utils stuff in https://github.com/dib-lab/charcoal/pull/203.