How to I use prefetch (SRAtoolkit) on multiple accessions all at one?
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6 weeks ago
biotrekker ▴ 100

I want to use prefetch from the SRAtoolkit (I downloaded using conda) for multiple accessions all at once. What is the best way to do this?

sratoolkit prefetch • 425 views
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No special trick. You could start multiple jobs with gnu parallel or a job scheduler via a for loop if you are on compute cluster. You will be limited to the network bandwidth available on the node/computer where you run it.

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6 weeks ago

What is the best way to do this?

use nf-core fetchngs: https://nf-co.re/fetchngs/1.12.0

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Do you know if this pipeline allows for multiple accessions all at once? Or does the download happen serially?

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If download links exist, the files will be downloaded in parallel

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