Minimap2: Clipping penalty [feature request]

[sjackman]

Could the clipping penalty similar to bwa mem -L be applied at the ends of sequences, and possibly also at the ends of scaffolds gaps (a run of nucleotides before a gap of Ns)?

[lh3]

Have you tried the --end-bonus option (see here)?

[sjackman]

No, I hadn't seen that option. Thanks, Heng! Would you suggest minimap2 -x asm10 --end-bonus=5 to achieve similar behaviour as bwa mem -x intractg?

[lh3]

Would you suggest minimap2 -x asm10 --end-bonus=5 to achieve similar behaviour as bwa mem -x intractg?

should be close.