How to I use prefetch (SRAtoolkit) on multiple accessions all at one?
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?
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Pierre Lindenbaum
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biotrekker •
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biotrekker •
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What is the best way to do this?
use nf-core fetchngs: https://nf-co.re/fetchngs/1.12.0
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Pierre Lindenbaum
If download links exist, the files will be downloaded in parallel
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No special trick. You could start multiple jobs with
gnu parallelor a job scheduler via aforloop if you are on compute cluster. You will be limited to the network bandwidth available on the node/computer where you run it.