Download FASTQs from ENA - BenLangmead/jhu-compute GitHub Wiki

On occasion we may want to download FASTQs from ENA rather than SRA.

This would mainly be because ENA supports 1) direct compressed FASTQ download 2) from an FTP. These features obviate the need of using SRA-tools to 1) download and 2) convert to FASTQ.

ENA also supports Globus:

https://www.ebi.ac.uk/about/news/service-news/read-data-through-globus-gridftp

However, not all SRA runs are available from ENA!

Quick example of a direct FASTQ sequence run download link via HTTP/FTP for a 6-digit run:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR204/ERR204946/ERR204946_1.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR204/ERR204946/ERR204946_2.fastq.gz

Single end, 7-digit run:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR101/006/SRR1016916/SRR1016916.fastq.gz

See the ENA examples page for more details: https://www.ebi.ac.uk/ena/browse/read-download