IUPAC symbol Y

[Liukvr]

Dear developers,
Many thanks for this very usefull tool. I have a question regarding DemuxFastqs. My barcode contains 4 IUPAC symbols (e.g. Y and R) but when tdemultiplexing they are counted ad mismatches. Is there a way to handle it without increasing --max-mismatches to 4?
Thanks in advance,
Luca

[nh13]

@Liukvr

1. See the fqtk demux tool that we prefer due to it being much much more performant. The DemuxFastqs was originally built to handle MiSeq size data. We would be more willing to add features to fqtk than DemuxFastqs, so I've created an issue there: Support IUPAC bases in the expected barcode fqtk#52
2. One temporary work-around would be to demultiplex using all the barcodes implied by the IUPAC bases, for example AANAA would be expanded into AAAAA, AACAA, AAGAA, and AATAA. Then you would demultiplex using the expanded list, and merge after. The unfortunate issue in this work-around is that only exact matching would be supported, hence the need for new functionality, which we would be more inclined to work on in fqtk (and with sponsorship!)

[Liukvr]

Thanks @nh13, very appreciated