Downloading read data

Sequencing reads are available for download through FTP and Aspara protocols in their original format and in an archive generated fastq formats described here.

Submitted data files

Submitted data files are organised by submission accession number under vol1/ directory in ftp.sra.ebi.ac.uk:
ftp://ftp.sra.ebi.ac.uk/vol1/<submission accession prefix>/<submission accession>

where <submission accession prefix> contains the first 6 letters and numbers of the SRA Submission accession. For example, the files submitted in the SRA Submission ERA007448 are available at: ftp://ftp.sra.ebi.ac.uk/vol1/ERA007/ERA007448/.

Archive generated fastq files

Archive generated fastq files are organised by run accession number under vol1/fastq directory in ftp.sra.ebi.ac.uk:
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/<run accession prefix>/<run accession>

where <run accession prefix> contains the first 6 letters and numbers of the run accession. For example, the archive generated fastq files for run ERR000916 are available at: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000916/.

Downloading files

We recommend the use of our file downloader application that can be used to download data files using study, sample, experiment or run accessions. This application can be used either interactively or from a command line and supports both FTP and a UDT based faster protocol.

The program can be downloaded from here.

Using wget

wget is a convenient way to download files over FTP.

Example:

wget  ftp://ftp.sra.ebi.ac.uk/vol1/ERA012/ERA012008/sff/library08_GJ6U61T06.sff 

Using aspera

Aspera ascp command line client can be downloaded here. Please select the correct operating system. The ascp command line client is distributed as part of the Aspera connect high-performance transfer browser plug-in.

Your command should look similar to this:

ascp -QT -l 300m -i <aspera connect installation directory>/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:<file or files to download> <download location>

or on Mac OSX:

ascp -QT -l 300m -i <aspera connect installation directory>/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:<file or files to download> <download location>

Note: The asperaweb_id_dsa.openssh public key was introduced in Aspera Connect plugin 3.3.3.  Earlier versions can still use asperaweb_id_dsa.putty.

Examples:

ascp -QT -l 300m -i /etc/aperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/ERA012/ERA012008/sff/library08_GJ6U61T06.sff /. 

ascp -QT -l 300m -i /etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/ERR036/ERR036000/ERR036000_1.fastq.gz .

ascp -QT -l 300m -i /etc/aperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/ERA012/ERA012008/sff/ /.

Latest ENA News

20 Aug 2014: Read data through Globus GridFTP
Read data can now be downloaded using Globus GridFTP through ebi#ena Globus Online public endpoint.

18 Aug 2014: Changes to SRA XML 1.5
Small changes to Experiment XML, Analysis XML, EGA Dataset XML, EGA DAC XMLs were deployed on 11th of August 2014.

1 Jul 2014: ENA release 120
Release 120 of ENA's assembled/annotated seqences now available

23 May 2014: Change to date format for advanced search
From 16th June 2014, the date format used in the advanced search will be changed to ISO format (YYYY-MM-DD).

20 May 2014: Update to the ENA SAMPLE checklist
From 10th of June 2014 the ENA SAMPLE checklist XML will be updated and the older version will be deprecated.