code: def _run_nucmer(self, ref, qry, outfile):
          '''Run nucmer of new assembly vs original assembly'''
          n = pymummer.nucmer.Runner(
              ref,
              qry,
              outfile,
              min_id=self.nucmer_min_id,
              min_length=self.nucmer_min_length,
              diagdiff=self.nucmer_diagdiff,
              maxmatch=True,
              breaklen=self.nucmer_breaklen,
              simplify=True,
              verbose=self.verbose
          )
          n.run(f _run_nucmer(self, ref, qry, outfile):
          '''Run nucmer of new assembly vs original assembly'''
          n = pymummer.nucmer.Runner(
              ref,
              qry,
              outfile,
              min_id=self.nucmer_min_id,
              min_length=self.nucmer_min_length,
              diagdiff=self.nucmer_diagdiff,
              maxmatch=True,
              breaklen=self.nucmer_breaklen,
              simplify=True,
              verbose=self.verbose
          )
          n.run()
docs: Run nucmer of new assembly vs original assembly