Can any software download tuberculosis short-reads from web the using a given name of sample or somehow?
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6.8 years ago
vassialk ▴ 200

Can any software download tuberculosis whole genome short-reads from the web using a given name of sample or somehow?

sequencing software tuberculosis • 1.4k views
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6.8 years ago
venu 7.0k

Did you check NCBI - SRA. Type Tuberculosis in search tab and you will get the results like this

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I could find http://www.ncbi.nlm.nih.gov/sra/?term=tuberculosis+belarus, thank you. How to get all short-reads from Belarus tub samples automatically or somehow?

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First hit of the link in my previous comment.

http://www.ncbi.nlm.nih.gov/sra/ERX1055122[accn] -> Organism - Mycobacterium tuberculosis

Downloading data:

This is an excellent tutorial by Obi Griffith, that helps you in downloading data from SRA. Have a look at it. But you may get problems in installing SRA toolkit depending on your OS, but I assure you, with little time you can overcome.

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