How to I use prefetch (SRAtoolkit) on multiple accessions all at one?

Question

[biotrekker]

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?

[GenoMax]

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.

Answer 1

[Pierre Lindenbaum]

What is the best way to do this?

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

[GenoMax]

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

[Pierre Lindenbaum]

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