Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Open
mikerobeson opened this issue Jun 8, 2023 · 2 comments · May be fixed by #100
Open

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

mikerobeson opened this issue Jun 8, 2023 · 2 comments · May be fixed by #100

Comments

@mikerobeson
Copy link
Member

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
Copy link
Member Author

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

@colinbrislawn
Copy link
Contributor

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
Development

Successfully merging a pull request may close this issue.

2 participants