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Old 06-21-2019, 08:02 AM   #1
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Location: UTSW

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Default Download all assemblies in a bioproject

Dear SEQanswers community,

I am trying to download all the assembly in a bioproject: Can anyone tell me how to download them all without manually copying the link and download the assembly like this: wget --recursive -e robots=off --reject "index.html" --no-host-directories --cut-dirs=6 ./

Any info will be greatly appreciated!


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Old 06-21-2019, 10:04 AM   #2
Richard Finney
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Here's an easy way to do it, though not quite a one liner ...

1) go to the "run selector" for your project of interest:

2) Download "runinfo table" (to a file called SraRunTable.txt )

3) create url based on SRR id . example: wget , use these URLS to wget in a script , like this ...

cat SraRunTable.txt | cut -f10 | awk '{print "wget"substr($1,1,6)"/"$1"/"$1".sra"}' | bash

Note that "cut -f10' is the field with the SRR ids.

Last edited by Richard Finney; 06-21-2019 at 10:14 AM.
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Old 06-21-2019, 11:05 AM   #3
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Cross posted and answered on Biostars:
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