you should find genes that cause this resistance to fluoroquinolone(ciprofoxin)in s.penemonia.then go to ncbi and choose SNP and type name of this gene,now you have all SNP of this gene

You should downloaded the related sequences from NCBI and analyze by Bioedit.

Thanks Parastou Rahimizadeh and Raghvendra Singh for your valuable time but my metor said you have to work on linux platform by using NGS pipline. I found sequence which Accession no is SRP000185 but dont know what to do even I dont know that this is right sequence or not.

hi Vishal,

I think your boss is talking about mutation analysis using NGS platform. For that as Parastou said, first you should find the gene responsible for the ciprofoxin resistance in s.penemonia and do sequencing of that gene. And then using open source NGS tools (I can suggest you Galaxy as its user friendly for beginners and open access ) you can identify the SNV and SNP's.

Thank you Logambiga Prakash, Yes he was talking about mutation but I dont want to use Galaxy. I want to use offline NGS tools. How to start process.

Once you obtain your sequence, you have 3 main objectives to do so.

Alignment

Variant calling

Annotation.

For all 3 steps, many offline tools are available. You may read some basic NGS analysis papers, so that you can get an idea on which tools to select. I have attached a paper on various tools used in NGS analysis for variant detection. Hope it may help you.

Thanks again Prakash, yes this papaer is seriously helpful. Prakash can I ask you one question? How should I find that no work has done on S.pneumoniae resistent against ciprofoxcin antibiotic. Thanks again