[MRG] use and report ANI from tax genome summarization
#2005
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12 tasks
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@ctb I think this is ready for review. Please suggest any additional tests or anything it may need! |
bluegenes
changed the title
tax genome summarization?tax genome summarization?
bluegenes
changed the title
tax genome summarization?tax genome summarization
|
realized I need to add some docs... will try to do asap :) |
ctb
requested changes
Jul 24, 2022
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I did a thing, successfully! The following: sourmash gather podar-ref/63.fa.sig gtdb-rs207.genomic-reps.dna.k31.zip
sourmash tax genome --gather-csv 63.x.gtdb.csv --taxonomy-csv gtdb-rs207.taxonomy.csv --ani 0.9yielded: |
ctb
reviewed
Jul 24, 2022
ctb
approved these changes
Jul 24, 2022
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(starting from #1788)
Add$cANI$ >= threshold, e.g.
--ani-thresholdtosourmash tax genome, to allow classification based on.95.Thoughts/warnings:
containment, because ANI was not yet implemented. I've left containment as the default here, but this might be something we want to change in the future.cANIhas different patterns based on the k-mer size and alphabet (moltype) used. Thresholds should be selected accordingly.