Question

How can I extract SNP from bacterial genome?

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5.3 years ago

k.kathirvel93 ▴ 300

HI EveryOne,

I Have a in-house pseudomonas aeruginosa bacterial whole genome data, and now i want to extract SNP from that. How can i do that ? Thanks in advance for any suggestions.

snp next-gen sequencing gene genome • 1.4k views

ADD COMMENT • link updated 5.3 years ago by shubhra.bhattacharya ▴ 140 • written 5.3 years ago by k.kathirvel93 ▴ 300

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The linked thread will help you to get started.

Bacterial SNP calling pipeline with SNP and indels confirmation

ADD REPLY • link 5.3 years ago by Arup Ghosh 3.2k

score 0 · Answer 1 · 2018-12-24

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5.3 years ago

shubhra.bhattacharya ▴ 140

The question is very broad. It does not give an idea about the objective of snp calling etc. Many online tutorials/papers etc are present in exhaustive fashion about the same.

You can read this for starters though: https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf

ADD COMMENT • link 5.3 years ago by shubhra.bhattacharya ▴ 140

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https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf

Is this protocol will help for p.aeruginosa also ?

ADD REPLY • link 5.3 years ago by k.kathirvel93 ▴ 300

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Yes, Use p.aeruginosa as your reference.

ADD REPLY • link 5.3 years ago by shubhra.bhattacharya ▴ 140