Question

SNPS finding for bacterial sequences

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6.2 years ago

hafiz.talhamalik ▴ 350

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 • 1.2k views

ADD COMMENT • link updated 6.2 years ago by h.mon 35k • written 6.2 years ago by hafiz.talhamalik ▴ 350

score 0 · Answer 1 · 2018-02-16

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6.2 years ago

h.mon 35k

SNP-sites is tailored exactly at your problem.

ADD COMMENT • link 6.2 years ago by h.mon 35k

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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 ?

ADD REPLY • link 6.2 years ago by hafiz.talhamalik ▴ 350