Given an input PAF file generated from minimap2 using a command something like this:
minimap2 -cx asm20 -t 32 --cs --secondary=no ref.fa query.fa | sort -k6,6 -k8,8Note the defauly implementation currently does not consider overlapping alignmnets. The -i flag does.
psd - Calculate the per-sequence divergence from a PAF file
Max Brown <[email protected]>
USAGE:
psd [-h] <PAF>
FLAGS:
-h, --help Prints help information
-i, --individual Print individual sequence divergence
values. These will be sorted by the
query input order.
ARGS:
<PAF> Path to PAF file