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Old 08-05-2013, 01:01 PM   #4
NGS group
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Join Date: Apr 2013
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Hi rhinoceros,

Thank you for your reply. The aim of my project is to distinguish outbreak strains, so I have to do the analysis by myself. The HAL pipeline is what I want exactly. However I am not so familiar with commend line, is there any other more user-freindly pipeline or programs under Windows system?

Victor
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Originally Posted by rhinoceros View Post
You could look around NCBI's ftp. Maybe your species is already in the SNP DB? If not, you might have to do all-vs-all blasts and clustering (maybe OrthoMCL) to find out the shared genes. What you want might be possible with eutils too. Oh and there's this pipeline called HAL that might do what you want..
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