map with defined number of mismatches

[Pol8]

Hi,

how can I map reads against the reference genome, so that I'm sure they align continuously, but allowing from 0 to 5 mismatches in the alignment?
Or alternatively find in the alignment, reads that map with 0 to 5 mismatches?

[Brian Bushnell]

BBMap has a "subfilter" flag - e.g. "subfilter=5" - which will ban alignments with more than 5 mismatches. It's a global aligner, so the reads will align continuously.