This repository contains a small tool to assess the accuracy of an assembly using minimap2.
It requires the pyvcf and pysam python packages, and minimap2 to be on your PATH.
fastmer.py --reference reference.fasta --assembly assembly.fasta --min-mapping-quality 10
assembly_name percent_identity qscore num_matches num_mismatches num_insertions num_deletions 4mer_acc 5mer_acc 6mer_acc 7mer_acc 8mer_acc 9mer_acc
nanopolish_r94 99.956154 33.58 4691618 163 730 1165 0.995 0.983 0.923 0.825 0.730 0.545