Matching Rate nextclade

[mcnaber]

Hello there,

I am working to edit the required matching rate for nextclade. My goal is to try and lower it to see a larger portion of my data sets and/or include alignments in my final result even if they don't meet the 0.300 minimum matching rate. Is there any way to edit this feature? I can't seem to find a command that controls this. Thank you.

[ivan-aksamentov]

Hi @mcnaber,

If you are using CLI, you can use --min-match-rate argument to set minimum seed matching rate. Read more in the built-in help:

nextclade run --help