Hi- I am using Mauve to export SNPs (but I am not sure why I get more SNPs than it is published before)- for example snps between 2 bacterial strains should be 500 but I get > 2000 snps- any advice why does this happen, please?
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Originally posted by mmmm View PostHi- I am using Mauve to export SNPs (but I am not sure why I get more SNPs than it is published before)- for example snps between 2 bacterial strains should be 500 but I get > 2000 snps- any advice why does this happen, please?
SNP calling can vary between tools depending on how you mask low complexity regions.
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Honestly I don't know, I'm not familiar with mauve algorithm.
have you tried with Mummer 3? http://mummer.sourceforge.net
I know Mummer can mask LCR.
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