Is the reference genome used when using the snp-sites software?

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

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Is the reference genome used when using the snp-sites software? #79

Closed youlijun closed 5 years ago

youlijun commented 5 years ago

Dear teacher： I found snp-site very good, but I have doubts. The input file I am using is coregene.aln generated by roary. Does it use the reference genome?Without a reference genome, how does it find snp? Thanks in advance

andrewjpage commented 5 years ago

More details are available in the paper http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056

You dont need a reference genome, if you 2 bases are different, then one of them must be a SNP.