I'm trying to find a strategy to call core SNPs in a collection of hundreds of bacterial genomes. I've been able to get some of them using kSNP tool Scalable SNP Analyses of 100+ Bacterial or Viral Genomes, but we think that tool is loosing many of them.
I'm thinking of using a reference-based method.
Thanks so much for your help, Best, Bernardo
Citation: Gardner SN, Slezak T (2010) Scalable SNP Analyses of 100+ Bacterial or Viral Genomes. J Forensic Res 1:107. doi:10.4172/2157-7145.1000107