I have assemblies of two microbial genomes from PacBio data (49 and 69 contigs each) and I'm trying to figure out how similar they are. The final genome size should be about 7.5 Mb.
I remembered the mummer tools from a project many years ago, so I ran nucmer and got the SNPs output using show-snps. This output turned out to be troublesome because it's not a VCF file. I was able to convert the SNPs using a script I found here.
- The mummer tools have been around for quite a while -- would you recommend something else, or are they still current?
- I heard bwa-mem can also now align whole microbial genomes -- anyone have any experience with this?
Thanks for any advice!