[MUMmer-help] summary statistics for draft assembly alignments?

[Jacqueline R M D. <jm...@pu...>]

Hi,

I have recently done a couple different assemblies of an avian genome and a reviewer has suggested aligning the two assemblies to the zebra finch genome and seeing which assembly aligns best.  The idea here is that the assembly that overlaps most closely with the zebra finch genome is probably the best one to use for downstream analyses.  I'd like to align each assembly to the zebra finch genome using nucmer and then generate some summary statistics like number of aligned/unaligned contigs, total aligned/unaligned length, percent of aligned bases, etc.  What is the best way to go about generating this type of data?  I found references to a script called "dnadiff" in the email help archives, but couldn't find the scrip referenced in the MUMmer 3 manual.

Best wishes...