How reads are downloaded

SRA reads are downloaded in the ".sra" format using the NCBI SRA-toolkit. A .sra file is typically 2.5x smaller than an equivalent zipped fastq file. Download uses the NCBI 'prefetch' utility, and the resulting file is read into the workbench using 'fastq-dump'.

Sometimes runs in SRA cannot be downloaded. The affected runs are listed in a Problems panel together with a description of the problem. It is still possible to download the remaining runs.

The most common problems are:

We support download of reads via the commercial FASP protocol from Aspera. In our testing, Aspera download is up to 10x faster than a normal http download.

To enable this functionality, you have to download the Aspera Connect software from

On Windows, choose to do a "Custom" install and choose to "Install for all users of this machine". You can then test if the installation worked by downloading a small file. The log (accessible from the Processes tab) will include the line "Downloading via fasp" if everything worked.

It is possible to change the Aspera options using Preferences | Advanced | SRA Download.

The following options are available: