Hi Mauvers,
After I've run a contig re-ordering step (on some draft assemblies), and
then used Progressive Mauve to align them against each other (and a related
reference), how would I get an overall percent identity between any of the
two, aggregated across any LCBs and contigs? I've thought of using the
positions in the SNPs file, but that excludes gaps between LCBs and other
more complicated differences, right?
Any help would be appreciated ...
~Joe
--
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
joseph.fass -at- gmail.com
530.752.2698 (w)
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