Extract just the region of each read that map to reference

Question

[bailliecharles]

Hi All, I want to map some fasta sequences to a reference, and only return the regions of the reads that map. The sequences are mostly very divergent from the reference and range from 600 - 30000bp. The reference is 300bp so I only want the 300bp from the queries that map to the reference. I've tried using MSA, but due to the differences in length of the queries trimming at either end can only really be done by eye. I was thinking bbmap/bbduk might have something?

Cheers, Charles