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  • SNP finder

    HI,

    i need a help in fininding out the SNP in while genome.. i have whole genome sequence of .acidophilus strain. mutant strain and wild type...which software i can use to find the SNP among this two whole genome sequence...


    regards

    roshan

  • #2
    there are many softwares like SNP detector, SNP browser. although I havent used anyone but just heard their names.

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    • #3
      Thanks for ur reply..i tried using SNP detector...however it was pretty hard for me operate it..so i was wondering if any other software available...

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      • #4
        Samtools is an excellent software to find NGS snps.

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        • #5
          thanks a lot :-)...this is helpful to me

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          • #6
            Bwa + gatk

            Hello there

            A college of mine did a lot of comparison between different combinations of aligners and SNP callers. If i remember correctly, he found that aligning the reads with BWA and using GATK to detect SNPs was the best way to go.

            I did not see any numbers on it, just heard it at the coffee table But i could be worth checking out if you have not looked at them before.

            This was on human samples i might add.

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