Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
17
gravatar for Phil Ewels
5 months ago by
Phil Ewels430
Sweden / Stockholm / SciLifeLab
Phil Ewels430 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

ADD COMMENTlink written 5 months ago by Phil Ewels430
2

Shopping basket/add files you need to collection

sra4

URLs

sra1

bash script

sra2

If you prefer .sra downloads

sra3

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax70k
1

Amazing! Works like a charm! Thanks so much!

ADD REPLYlink written 5 months ago by jean.elbers1.2k
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 5 months ago • written 5 months ago by ATpoint21k
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 5 months ago by Phil Ewels430
1

Cool, works fine!

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint21k
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