ENH: add support for the different versions of `uchime_denovo` within vsearch

qiime2 / q2-vsearch

vsearch plugin for QIIME 2

BSD 3-Clause "New" or "Revised" License

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ENH: add support for the different versions of `uchime_denovo` within vsearch #92

Open mikerobeson opened 1 year ago

mikerobeson commented 1 year ago

Somewhat an extension of #75, but there have been improvements to the uchime_denovo algorithm of vsearch. Specifically:

uchime2_denovo
uchime3_denovo

As outlined in the vsearch manual, these additional options are ideal for working with denoised amplicons. Also note that the minh option is ignored for these two options.

mikerobeson commented 8 months ago

Might be good to default to uchime3_denovo with option for abskew.

colinbrislawn commented 1 month ago

Supporting abskew is a good idea, but we may want to address that separately because

abskew also applies to uchime_ref
The only difference between uchime2_denovo and uchime3_denovo is their default abskew value, so I want to get --p-method working first