Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
28
gravatar for Phil Ewels
18 months ago by
Phil Ewels570
Sweden / Stockholm / SciLifeLab
Phil Ewels570 wrote:

Hi all,

As a fun little side project I've made a web tool to find runs on the NCBI Sequence Read Archive (SRA) and fetch the download URLs for these. You can do all of this in a couple of clicks, hopefully quite a bit easier than navigating the main SRA pages.

In addition to getting the SRA links the tool now queries the European Nucleotide Archive (ENA) for direct FastQ downloads and also provides these URLs.

All links are given as a simple list and also as a bash script which uses curl to download the data and gives nicer filenames that include the sample name in addition to its accession number.

You can find the tool here: https://ewels.github.io/sra-explorer/

It's open source and in fact just a single HTML file, built using AngularJS and Bootstrap. If you're curious, you can find the code here: https://github.com/ewels/sra-explorer

Phil


NOTE (added by genomax 16 Aug 2020) : sra-explorer is currently NOT working. Phil is aware of the issue and is planning to provide a fix in next couple of weeks.


Edit ( 6.5.2020 by ATpoint ) sra-explorer also (for quite some time now) supports creation of Aspera download links. This enables downloads often notably faster than ftp. Setting up Aspera is simple, for a tutorial on Aspera installation and some background also see Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD COMMENTlink modified 4 weeks ago by genomax89k • written 18 months ago by Phil Ewels570
2

Shopping basket/add files you need to collection

sra4

URLs

sra1

bash script

sra2

If you prefer .sra downloads

sra3

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax89k
3

Amazing! Works like a charm! Thanks so much!

ADD REPLYlink written 18 months ago by jean.elbers1.4k

Works great, very useful utility, thank you!

ADD REPLYlink written 12 months ago by hermidalc0
1

Very convenient, thank you, also for multiqc! You might consider adding an option to provide links for downloads driven by Aspera as in my tutorial Fast download of FASTQ files from the European Nucleotide Archive (ENA). That speeds up downloads notably.

ADD REPLYlink modified 18 months ago • written 18 months ago by ATpoint38k
1

Nice idea and great tutorial! I've just added this functionality - it would be great if you could have a look and make sure that I haven't made any errors.. Note that I added an option to append a mv command to rename the files. I've never used Aspera myself, so I hope this actually works!

ADD REPLYlink written 18 months ago by Phil Ewels570
1

Cool, works fine!

ADD REPLYlink modified 18 months ago • written 18 months ago by ATpoint38k
1

Is it possible that this tool is currently not working? Neither my own SRAs, nor just clicking on the examples provided is working. 😢 Thanks!

ADD REPLYlink written 4 weeks ago by Brunox1320
1

Yes - I’ve had a bunch of reports about problems over the past few days. I guess that an API endpoint changed somewhere. I’m on holiday at the moment but will take a look when I’m back. Apologies for the inconvenience!

ADD REPLYlink written 4 weeks ago by Phil Ewels570
1

Phil Ewels : Would it be possible add a note to sra-explorer main page that the tool is not currently working and you are going to fix it?

Edit: Main esearch call in sra-explorer seems to be working.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax89k

Not easily - I don’t have a computer with me. If I can edit code to add a notice on the web page then I can probably fix whatever the issue is :) I’ll be back home in a few days (though technically still on holiday) so will try to take a look then. If I can’t figure it out quickly then I’ll add a notice.

ADD REPLYlink written 4 weeks ago by Phil Ewels570

To follow - I managed to take a quick look in an evening over my holiday and it was not as trivial as I was hoping. I did manage to put up a notice though. I'll try to find some time to sit down with it in the next couple of weeks to do some code refactoring / rewriting and get it up and running again.

ADD REPLYlink written 10 days ago by Phil Ewels570

Much appreciated. Please let us know when you find a fix. This is the interface NCBI should have provided :-)

ADD REPLYlink modified 10 days ago • written 10 days ago by genomax89k

Nice tool...i used and works fine......👍🙏

ADD REPLYlink written 11 months ago by psschlogl30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 729 users visited in the last hour