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ngsfilter: how to represent degenerate primers in sample description file?
#1
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

GGYCTW

I'm thinking about putting the following into my sample description file
GG[CT]CT[AT]

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.
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#2
Hi,

Just use GGYCTW, ngsfilter is understanding IUPAC

All the best

Eric
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#3
Wow, very nice, thank you!

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