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ngsfilter: how to represent degenerate primers in sample description file?
When using ngsfilter, I want it to be able to search for degenerate primers.

I was wondering if I can use regex in the sample description file that is referenced by ngsfilter?

If yes, what flavor of regex can I use?  POSIX?  PERL?

Otherwise, does ngsfilter understand the IUPAC ambiguity code?  

The universal COI primers developed by Leray et al for metabarcoding are highly degenerate.  Consequently, there has to be a way to search allow for multiple matches at certain positions. 

Let's say my primer is


I'm thinking about putting the following into my sample description file

I know that I could set the -e argument to specify the number of mismatches, but that's not an elegant solution with 10 in 26 positions being degenerate.

Just use GGYCTW, ngsfilter is understanding IUPAC

All the best

Wow, very nice, thank you!

That would be relevant information to include in the ngsfilter documentation.

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