This script is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species.

Output files:

• report: Summary of alignments, differences and SNPs
• delta: Standard nucmer alignment output
• 1delta: 1-to-1 alignment from delta-filter -1
• mdelta: M-to-M alignment from delta-filter -m
• 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
• mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
• snps: SNPs from show-snps -rlTHC .1delta
• rdiff: Classified ref breakpoints from show-diff -rH .mdelta
• qdiff: Classified qry breakpoints from show-diff -qH .mdelta