Ena short read archive download

The first entry in the tuple contains the filenames which you might need later in your application , the second contains a list of paths on the ENA servers where those files can be found. The solution for these reads is to download the data manually from the ftp location. Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group.

Create a free Team What is Teams? Learn more. Asked 3 years, 6 months ago. Active 3 years, 6 months ago. Viewed times. My bash script looks like this requires aspera ascp and fastq-dump and I wanted to make changes that are commented now!

Is there an easy way how to download reads from ENA knowing just the accession number? Improve this question. Kamil S Jaron. Add a comment. The above command would download the Run SRR Run accessions are the end of the line 1-to-1 relationship.

Installation and setup of Aspera Connect is out of the scope of this documentation, but I can assure you its a simple installation. The above command will attempt to download SRR using the ascp tool. By default it will try to use the private key file that is included during the Aspera Connect installation. Skip to content. This repository has been archived by the owner.

It is now read-only. Star 0. Branches Tags. Could not load branches. The run submission holds information about the raw read files generated in a run of sequencing as well as their location on an FTP server. The experiment submission holds metadata that describe the methods used to sequence the sample.

If you are not yet familiar with the metadata model, please see here for some more information. As a raw read submission references ENA sample and study objects, you must submit these before you can submit your read data.