Download fastq from EBI using Aspera

Ji Huang 2024-01-26 1 min read

This post shows you how to download the fastq files from EBI, if they are available. The Aspera speeds up the downloading process by a LOT!

I use the Aspera on NYU HPC, but it should work on your own device too.

Get the openssh key path. I found it at /share/apps/aspera/4.1.3.93/etc/asperaweb_id_dsa.openssh

module show aspera/4.1.3.93
cd /share/apps/aspera/4.1.3.93/etc

Get the downloading link. Go to https://sra-explorer.info/#, paste the library info. Modify the ascp openssh key path.
Copy the generated script and save it on HPC. Remember to add module load aspera/4.1.3.93 to the script.
Run the script from the Data Transfer Node. ssh gdtn