I have sequenced some DNA fragments (with nanopore) that had been previously barcoded with a barcode like this:
so basically it is made by 3 different barcodes separated by 10 random nucleotides:
Barcode1 - 10Ns - Barcode2 - 10Ns - Barcode3
I'm looking for an alignment tool that takes in account the presence of the Ns (wildcards) in order to detect the reads that incorporate this barcode. Also, since I used nanopore for sequencing, the reads produced are full of fake indels, so the aligner should also allow the presence of little gaps (1-3 bp), or it should be possible to adjust the gap penalty.
Thank you very much in advance!