SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Primers for Trinity assemblies FelipeAd Illumina/Solexa 0 05-09-2016 03:37 AM
Combining two different assemblies yekwah De novo discovery 1 07-27-2013 05:12 AM
Miseq assemblies RGLADSTONE Bioinformatics 1 01-11-2013 02:25 AM
velvet assemblies rahularjun86 Bioinformatics 3 01-31-2012 02:59 AM
How are you comparing assemblies? Hobbe Bioinformatics 0 02-17-2011 10:38 PM

Reply
 
Thread Tools
Old 06-21-2019, 07:02 AM   #1
dazhudou1122
Junior Member
 
Location: UTSW

Join Date: Aug 2016
Posts: 3
Default 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
dazhudou1122 is offline   Reply With Quote
Old 06-21-2019, 09:04 AM   #2
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 701
Default

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 09:14 AM.
Richard Finney is offline   Reply With Quote
Old 06-21-2019, 10:05 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,953
Default

Cross posted and answered on Biostars: https://www.biostars.org/p/385930/
GenoMax is offline   Reply With Quote
Reply

Tags
assembly

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:08 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO