Restrictive alignment with minimap2
I need to align nanopore reads from human to a custom reference genome and I want to align only the reads that have a very high identity. I tried changing the missmatch penalty but if I increase it too much minimap raises a Segmentation fault error. Should I change something else in the configuration of minimap2 or should I filter the aligned reads by score or something and how would I do that?
Thank you!
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