Download all assemblies in a bioproject

dazhudou1122 · 06-21-2019, 08:02 AM

Dear SEQanswers community,

I am trying to download all the assembly in a bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=474907 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 ftp://ftp.ncbi.nlm.nih.gov/genomes/a....1_ASM479397v1 ./

Any info will be greatly appreciated!

Best,

Wenhan

Richard Finney · 06-21-2019, 10:04 AM

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:

https://www.ncbi.nlm.nih.gov/Traces/...re&query_key=2

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

3) create url based on SRR id . example: wget ftp://ftp-trace.ncbi.nih.gov/sra/sra.../SRR001115.sra , use these URLS to wget in a script , like this ...

cat SraRunTable.txt | cut -f10 | awk '{print "wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/"substr($1,1,6)"/"$1"/"$1".sra"}' | bash

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

GenoMax · 06-21-2019, 11:05 AM

Cross posted and answered on Biostars: https://www.biostars.org/p/385930/

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06-21-2019, 08:02 AM	#1
dazhudou1122 Junior Member Location: UTSW Join Date: Aug 2016 Posts: 3	Download all assemblies in a bioproject Dear SEQanswers community, I am trying to download all the assembly in a bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=474907 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 ftp://ftp.ncbi.nlm.nih.gov/genomes/a....1_ASM479397v1 ./ Any info will be greatly appreciated! Best, Wenhan

06-21-2019, 10:04 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	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: https://www.ncbi.nlm.nih.gov/Traces/...re&query_key=2 2) Download "runinfo table" (to a file called SraRunTable.txt ) 3) create url based on SRR id . example: wget ftp://ftp-trace.ncbi.nih.gov/sra/sra.../SRR001115.sra , use these URLS to wget in a script , like this ... cat SraRunTable.txt \| cut -f10 \| awk '{print "wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/"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.

06-21-2019, 11:05 AM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Cross posted and answered on Biostars: https://www.biostars.org/p/385930/