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jfjlaros / demultiplex

Versatile FASTA/FASTQ demultiplexer.
MIT License
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Degenerated constructs #24

Closed iquasere closed 2 years ago

iquasere commented 2 years ago

Greetings!

I was wondering if demultiplex can work with degenerate constructs, e.g. TTMTRGRACAGGCTCCTC.

jfjlaros commented 2 years ago

I think it will work, but since the internal aligner has no notion of this, comparing a degenerate base to one of its possibilities will result in a mismatch. E.g., N vs. A will result in a mismatch, just like T vs. A will.

Perhaps you can increase the number of allowed mismatches if you want to compensate for this.

iquasere commented 2 years ago

Thank you for clarifying! Also, does demultiplex support multithreading?

jfjlaros commented 2 years ago

I am afraid it does not.

iquasere commented 2 years ago

Thank you for the informations!

jfjlaros commented 2 years ago

You're welcome.