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SRA Application Notes [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.

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SRA Application Notes [Internet].

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SRA Usability Changes 2010-11-17 (Deprecated)

Active Date2010-11-18
Inactive Date2012-05-18

1 Overview

The SRA web site has changed in important ways.

  • Static fastq dumps for every run have been removed from the site. Instead users are asked to download the run in archive format and execute a dump of data on their local system.
  • The web site Study, Sample, Analysis report pages have been changed
  • The Run Browser has been changed
  • A new SRA Object search function has been added.

2 Static fastq dumps removed

NCBI has been provisioning text dumps of SRA runs for the past two years. These dumps are executed on a scheduled basis and provide an Archive view of the data, including splitting of mate pair reads into separate files.

The size of this service has now outstripped the ability to store it so it has been removed. From now on, users are asked download runs of interest and execute dumps into the desired format using the SRA SDK toolkit available at .

The advantage of this approach is that users can select which format to dump to, can be assured that the data are available soon after loading, and can be assured that the submitter corrections have been applied to their datasets.

Data sets that are available for download through aspera or ftp can be reached this way from the Entrez search result:

Download reads for this experiment in sra or sra-lite formats 

SRA data are provisioned in full "sra" format and "sra-lite" format objects. With "sra-lite" it is possible to extract sequence and qualities (for example, fastq format). Intensity scores are provided only in the full "sra" format. Extraction of SFF format should begin with full "sra" formatted SRA objects so that the flowgram can be included in the SFF file.
To get "fastq" format see Converting SRA format data into FASTQ in the SRA Handbook.

3 Summary of Web Site Changes

3.1 New SRA Object search function

It is now possible to submit to Entrez SRA a search time and have it return a table of hits organized by SRA object type. Here is an example with the general text search term “HMP”:


This query returned hits in both the open (public access) and protected (controlled access) SRAs. Click through any of these hit links in order to access Entrez reports for each type of object.

3.2 Browse/Studies, Samples, Analyses tables updated


Removed link in title (no hyperlink)


Replaced the link under Accession with the hyperlink previously under Title.


Removed all FASTQ download links

3.3 Browse/Studies, Samples, Analyses separate item


Removed links from Accession on title line for Studies, Samples and Analyses


Submission link has been removed


Added Entrez Docsum


Added help line/link

Image Site_changes.jpg

3.4 Browse/Run Browser updates


Removed X and Y coordinate search from Run Browser result page

Image Removed_download.jpg

4 Bulk Downloads

4.1 Linux Aspera Bulk Download

It is possible to download a run, experiment, sample, or study using the fasp protocol in Linux. A command template for Aspera using the ‘ascp’ utility is:

ascp -i <key> -QT -L <logdir> -l 100m<src> <dest>


key    = <aspera install directory>/aspera/etc/asperaweb_id_dsa.putty
logdir = directory that contains ‘aspera-scp-transfer.log’ which can be used for
resumption of an interrupted transfer

src = source directory or file being downloaded
dest = destination directory for download

An example command for Linux is:

ascp -i /opt/aspera/etc/asperaweb_id_dsa.putty -QT -L . –l 100m /tmp

4.2 Windows Aspera Bulk Download

It is possible to use Aspera to download a run, experiment, sample, or study using the fasp protocol on Windows. The template for Aspera using the ‘ascp’ utility is the same except you need a complete path to the ‘ascp’ utility:

"C:\Program Files\Aspera\Aspera Connect\bin\ascp" -i <key> -QT -L 
<logdir> -l 100m<src> <dest>


key    = "<aspera install directory>\Aspera\Aspera Connect\etc\asperaweb_id_dsa.putty"

See ‘Linux Aspera Bulk Download’ for explanation of logdir, src, and dest.

An example command for Windows is:

"C:\Program Files\Aspera\Aspera Connect\bin\ascp" -i "C:\Program Files\Aspera\Aspera Connect\etc\asperaweb_id_dsa.putty"
-QT -L "C:\Program Files\Aspera\Aspera Connect\var\log"
/ars/:vog.hin.mln.ibcn.ecart-ptf@ptfnonasra-instant/reads/ByExp/litesra/SRX/SRX000/SRX000007/SRR000001 C:\Temp

4.3 FTP Download

You can use to transfer runs using the ftp protocol. For example, to download ‘SRR000001.lite.sra’ after logging into, use this directory:

Bookshelf ID: NBK49286


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