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Old 12-11-2011, 07:49 PM   #1
roshanbernard
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Default 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
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Old 12-12-2011, 02:07 AM   #2
AsoBioInfo
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there are many softwares like SNP detector, SNP browser. although I havent used anyone but just heard their names.
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Old 12-12-2011, 04:49 AM   #3
roshanbernard
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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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Old 12-12-2011, 05:06 AM   #4
yqzhu
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Samtools is an excellent software to find NGS snps.
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Old 12-15-2011, 04:26 PM   #5
roshanbernard
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thanks a lot :-)...this is helpful to me
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Old 12-16-2011, 12:46 AM   #6
dahlo
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Default 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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