How can I identify the positions and number of SNPs in a set of genomes?

20 April 2020 1 7K Report

I have 56 genome sequences aligned to one reference genome sequence. Now i want to identify the number of SNPs throughout the genomes, their positions to compare between the 56 query genomes. Is there any software or web based tool to do that?

Arsh Shrikant Chavan

You can use 'Breseq'. I used it to identify SNPs from the WGS data of E.coli. Worked pretty well for me

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