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use ncbi/ngs library to slurp in SRA reads #17

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BenLangmead opened this issue Mar 5, 2015 · 1 comment
Open

use ncbi/ngs library to slurp in SRA reads #17

BenLangmead opened this issue Mar 5, 2015 · 1 comment

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@BenLangmead
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This Python module seems to be a reasonably easy-to-use and portable way to slurp a stream of reads from the SRA: https://github.com/ncbi/ngs/tree/master/ngs-python.

It depends on a library that they will dynamically download and install in ~/.ncbi upon first use of the LibManager module:

https://github.com/ncbi/ngs/blob/master/ngs-python/ngs/LibManager.py

There's many-second delay when this happens. Overall, I don't see anything terribly wrong with that way of doing things.

It's written by US govt employees and as such isn't copyrighted. I'm pretty sure, but not 100% positive, that makes it OK to package in an open source project.

Final note: I thought that DNANexus mirrored the SRA, but it seems they only mirror the SRA metadata. So this library is only for accessing reads at NCBI, and there is no mirror that I know of.

@BenLangmead BenLangmead changed the title use ncbi/ngs library to such in SRA reads use ncbi/ngs library to slurp in SRA reads Mar 5, 2015
@BenLangmead
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This is low priority

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