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SNPS finding for bacterial sequences

any software for snp calling for baterial data. I have about 300 bacterial sequences and i have done multiple sequence alignment. I want to find SNPs in them. kindly guide me about the pipeline and softwares as well. Regards

snp snp
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updated by h.mon h.mon • written by hafiz.talhamalik hafiz.talhamalik

1 answer

SNP-sites is tailored exactly at your problem.

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written by h.mon h.mon

I have used this.. but vcf file generated by SNP-sites has allignment issues. also why its not taking any reference file to generate vcf ?

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written by hafiz.talhamalik hafiz.talhamalik

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