SRA News

SRA Software Toolkit 2.3.1 has been released

Fri, 08 Mar 2013 14:00:00 EST

NCBI has released SRA Toolkit 2.3.1. This version eases remote access to SRA files including compressed aligned sequence files that previously required downloading their reference files, by automatically downloading the needed data and files. The new version also includes a GUI Java configuration interface that can be run from X-Windows on Linux, and enhancements to previously released binaries.

Users can download the latest software from NCBI SRA software page. For technical assistance please contact the SRA Development team at sra-tools@ncbi.nlm.nih.gov

Scheduled SRA Service Interruption

Thu, 13 Dec 2012 09:00:00 EST

SRA data submissions will be interrupted starting on December 14th from 9 pm until December 16th at 5 pm due to scheduled maintenance. Entrez and SRA search will continue to function during this time. Please schedule your submissions and downloads accordingly.

SRA Toolkit 2.2.2 has been released

Thu, 13 Dec 2012 09:00:00 EST

NCBI has released SRA Toolkit version 2.2.2. This release includes minor bug fixes to previous release version 2.2.0. SRA Toolkit precompiled binaries and source code are available from the Software page on the SRA web site. For technical questions please contact the SRA development team sra-tools@ncbi.nlm.nih.gov

CGHub to Host TCGA Dataset

Fri, 20 Apr 2012 11:00:00 EST

As of May 1, 2012, the Cancer Genomics Hub (CGHub) will be hosting the TCGA dataset, and all downloads of TCGA data must take place via this service. For more information, visit the CGHub website.

NCBI Sequencing Archive of TCGA Data Has Been Extended Until April 30, 2012

Wed, 07 Mar 2012 16:00:00 EST

TCGA has arranged with NCBI to temporarily extend maintenance of the TCGA data in the Sequence Read Archive (SRA). Users may continue to download TCGA data from NCBI until April 30, 2012. All requests for data retrieval must be submitted by April 29, 2012, and all data downloads must be completed by April 30, 2012. After April 30, NCBI will no longer host sequencing data from TCGA in the SRA. Users can sign up for updates for future TCGA data releases and other TCGA-related information.

For immediate issues, email TCGA@mail.nih.gov. Requests for correction or update of TCGA data and metadata should be directed to the TCGA program at TCGA@mail.nih.gov.

NCBI Sequencing Archive of TCGA Data Has Been Extended

Thu, 16 Feb 2012 16:15:00 EST

TCGA has arranged with NCBI to temporarily extend maintenance of the TCGA data in the Sequence Read Archive (SRA). Users may continue to download TCGA data from NCBI until March 31, 2012. All requests for data retrieval must be submitted by March 30, 2012, and all data downloads must be completed by March 31, 2012. After March 31, NCBI will no longer host sequencing data from TCGA in the SRA. Users can sign up for updates for future TCGA data releases and other TCGA-related information.

For immediate issues, email TCGA@mail.nih.gov

30X coverage dataset from the Denisovan hominin individual is now available in the SRA

Mon, 13 Feb 2012 13:00:00 EST

A 30X coverage dataset from the Denisovan hominin individual is now available in the SRA

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=ERP000318

This dataset is originally referenced in the Nature publication

http://www.ncbi.nlm.nih.gov/pubmed/21179161

with additional coverage just provided by the Denisova Genome Consortium.

SRA Software Toolkit 2.1.9 has been released

Tue, 10 Jan 2012 18:00:00 EST

SRA Toolkit 2.1.9 precompiled binaries and source code are available from the Software page on the SRA web site. This release includes improvements to the SRA BAM loader and sam-dump. For technical questions please contact the SRA development team sra-tools@ncbi.nlm.nih.gov

Updated script for downloading reference sequences supporting cSRA format

Fri, 06 Jan 2012 18:00:00 EST

Please download the updated configuration-assistant.perl script for use with SRA Toolkit. Due to firewall issues, the URI of reference sequences is changed which requires changes in the configuration-assistant.perl script. This script helps users download reference sequence files needed for decompressing NCBI cSRA format files that are created from BAM files. Other format files that do not include alignment data are not affected by this change.

NCBI Sequencing Archive of TCGA Data Has Been Further Extended

Tue, 20 Dec 2011 16:00:00 EST

TCGA has arranged with NCBI to temporarily extend maintenance of the TCGA data in the Sequence Read Archive (SRA). Users may continue to download TCGA data from NCBI until February 29, 2012. All requests for data retrieval must be submitted by February 28, 2012, and all data downloads must be completed by February 29, 2012. After February 29, NCBI will no longer host sequencing data from TCGA in the SRA. Users can sign up for updates for future TCGA data releases and other TCGA-related information.

For immediate issues, email TCGA@mail.nih.gov

SRA Software Toolkit 2.1.8 has been released

Tue, 06 Dec 2011 20:00:00 EST

SRA Toolkit 2.1.8 precompiled binaries and source code are available from the Software page on the SRA web site. This release includes the SRA BAM loader, enhancements to sam-dump and existing SRA readers and writers. In addition the dbcc software now outputs messages in verbose mode by default. Please note that going forward, NCBI will only support NCBI pre-built Windows binaries; Windows source code is no longer supported. NCBI still supports the source code for Linux and Mac versions. For technical questions please contact the SRA development team sra-tools@ncbi.nlm.nih.gov

Update: NCBI Sequencing Archive of TCGA Data Has Been Extended

Wed, 09 Nov 2011 10:00:00 EST

TCGA has arranged with NCBI to temporarily extend maintenance of the TCGA data in the Sequence Read Archive (SRA). Users may continue to download TCGA data from NCBI until December 31, 2011. All requests for data retrieval must be submitted by December 28, 2011, and all data downloads must be completed by December 31, 2011. After December 31, NCBI will no longer host sequencing data from TCGA in the SRA. Users can sign up for updates for future TCGA data releases and other TCGA-related information. For immediate issues, email TCGA@mail.nih.gov

Status of the NCBI Sequence Read Archive (SRA)

Fri, 14 Oct 2011 11:00:00 EST

Subsequent to an announcement in February 2011 that NCBI was planning to phase out the SRA due to funding constraints, NIH support has been provided that will enable the continuation of SRA. NCBI will continue to operate the SRA as NIH’s primary archive of high-throughput sequencing data and as part of the international partnership of archives at the NCBI, the European Bioinformatics Institute and the DNA Database of Japan. Data submitted to any of the three organizations are shared among them. The SRA is managing high-throughput sequencing data from many large studies funded by NIH Institutes. The SRA will also continue to archive high-throughput sequencing data that are associated with: 1. RNA-Seq, ChIP-Seq, and epigenomic data that are submitted to GEO
2. Genomic and transcriptomic assemblies that are submitted to GenBank
3. 16S ribosomal RNA data associated with metagenomics that are submitted to GenBank It is NCBI's policy to make its publicly available data, including that in the SRA, available to others for redistribution so that they can provide value added services, such as tool sets for analyzing data and alternate interfaces. NCBI will continue work on new approaches for optimum storage and retrieval of raw sequencing data and their alignments.

SRA Software Toolkit 2.1.7 has been released

Tue, 11 Oct 2011 18:00:00 EST

Toolkit 2.1.7 precompiled binary files and source code for the release are available from the Software page on SRA web site. This release includes new features for BAM and SAM support. For more information on how to use the new features please refer to the release notes and Software Documentation on the Software section of the SRA site.

Update: NCBI Sequencing Archive of TCGA Data

Tue, 27 Sep 2011 15:00:00 EST

TCGA has arranged with NCBI to temporarily extend maintenance of the TCGA data in the Sequence Read Archive (SRA). Users may continue to download TCGA data from NCBI until November 27, 2011. All requests for data retrieval must be submitted by November 27, 2011, and all data downloads must be completed by November 30, 2011. After November 30, NCBI will no longer host sequencing data from TCGA in the SRA. Users can sign up for updates for future TCGA data releases and other TCGA-related information here (http://cancergenome.nih.gov/abouttcga/peoplecontacts/emailsignup). For immediate issues, email TCGA@mail.nih.gov.

NCBI Implements Compression by Reference

Wed, 14 Sep 2011 10:00:00 EST

Compression by Reference is a sequence alignment compression process for storing sequence data. Currently BAM, Complete Genomics and Illumina export.txt formats contain alignment information. Compression by Reference only stores the difference in base pairs between sequence data and the segments it aligns to. The decompression process to restore original data such as FastQ dump would require fast access to the actual sequences of the references. NCBI recommends that SRA users dedicate local disk space to store local references downloaded from the NCBI SRA site. Linked references should be in a location accessible by the SRA Reader software.

Older files in the NCBI system may not have been compressed using Compression by Reference. For more information on how to use Reference-based compressed files, download local references, and use related tools please refer to the "Compression by Reference Readme" file on the NCBI SRA website

SRA Toolkit 2.1.5 has been released

Fri, 09 Sep 2011 16:00:00 EST

Precompiled binary files as well as the source code for the release are available from the SRA software site. This release includes minor bug fixes to samdump which includes optimization of Compression by Reference.

Change of Center_name from WIBR to BI

Fri, 09 Sep 2011 16:00:00 EST

Trace Archive submissions from Whitehead Institute for Biomedical Research (WIBR) are now listed under a center_name of Broad Institute (BI). Searches for traces submissions previously from WIBR will need to be updated to reflect this change.

SRA Toolkit 2.1.4 has been released

Fri, 02 Sep 2011 10:00:00 EST

Precompiled binary files as well as the source code for the release are available from the SRA software site. This release includes minor bug fixes and optimization of Compression by Reference, which is a sequence alignment compression process for storing sequence data. For more information on how to use this feature please refer to the Compression by Reference Readme file: http://trace.ncbi.nlm.nih.gov/Traces/sra/std

SRA Toolkit 2.1.3 Released

Fri, 26 Aug 2011 17:00:00 EST

SRA Software Toolkit 2.1.3 has been released. Precompiled binary files for common operating systems as well as the source code for the release are available from the software page of SRA. This release includes support for Compression by Reference, which is a sequence alignment compression process for storing sequence data. For more information on how to use the new features please refer to the Compression by Reference Readme file: http://trace.ncbi.nlm.nih.gov/Traces/sra/std

FTP Address Changes

Mon, 22 Aug 2011 11:00:00 EST

In our continuing efforts to streamline processes and improve performance the following NCBI FTP servers will be restricted to their designated access:

ftp-private.ncbi.nlm.nih.gov is for all ftp submission uploads only
ftp-trace.ncbi.nlm.nih.gov is for downloads of SRA and 1000 Genome files
ftp.ncbi.nlm.nih.gov is for downloads of all other types of data

While in the past uploads have not been blocked to ftp and ftp-trace, we will be enforcing this requirement.

NCBI will no longer archive new sequencing data from TCGA in the Sequence Read Archive

Wed, 17 Aug 2011 12:00:00 EST

NCBI will no longer archive new sequencing data from TCGA in the Sequence Read Archive. The release of dbGaP's TCGA study phs000178 version 5 on August 15, 2011 constitutes the up-to-date and final compendium of files available at NCBI. All requests for data retrieval must be submitted by September 27, 2011, and all data downloads must be completed by October 1. Users can sign up for updates for future TCGA data releases and other TCGA-related information at: http://cancergenome.nih.gov/abouttcga/peoplecontacts/emailsignup. For immediate issues, email TCGA@mail.nih.gov.

SRA Documentation Update

Wed, 17 Aug 2011 10:00:00 EST

Documentation for the Download Guide has been updated to reflect the latest features and changes to the SRA Toolkit version 2.1.2. An Application Note has also been added for the XML Schema 1.3 release.

SRA XML Schema 1.3 installed

Thu, 11 Aug 2011 18:00:00 EST

The SRA xml schema 1.3 has been installed. Please see full release notes at http://www.ncbi.nlm.nih.gov/books/NBK56555/ This schema includes new platforms and instrument models.

SRA Toolkit 2.1.2 Released

Wed, 27 Jul 2011 11:00:00 EST

SRA Software Toolkit 2.1.2 has been released. Precompiled binary files for common operating systems as well as the source code for the release are available from the software page of SRA. The update includes bug fixes as well as new features.

SRA surpasses 100 Terabases

Mon, 27 Jun 2011 14:00:00 EST

The NCBI Sequence Read Archive (SRA) holdings recently surpassed 100 Terabases of

open-access genetic sequence reads from next generation sequencing technologies.

This figure includes substantial contributions mirrored from INSDC partner SRA databases at the European Bioinformatics Institute and the DNA Data Bank of Japan.

This figure does not include capillary sequencing data currently stored in the Trace Archive.

Maintenance Outage

Fri, 10 Jun 2011 11:00:00 EST

NCBI servers will undergo maintenance beginning June 11 at 7 AM EDT and plan to return to full operation by 4PM EDT. During this time, NCBI services, including Pubmed, BLAST and the Entrez search and retrieval systems, will be operational but may have slower performance. Data submission systems, including GenBank FTP submissions, SequinMacroSend, dbGaP, SRA, Trace and GEO submission systems, will be unavailable. dbGaP and SRA retrieval will not be available during this time as well. Please contact NCBI with concerns: info@ncbi.nlm.nih.gov

European E. coli O104:H4 Outbreak Data Released

Fri, 10 Jun 2011 10:00:00 EST

Two isolates of Escherichia coli O104:H4 have been released on SRA

http://www.ncbi.nlm.nih.gov/sra/SRP006916

http://www.ncbi.nlm.nih.gov/sra/SRP007080

SRA Status Update

Tue, 10 May 2011 16:00:00 EST

SRA Archive is still in service.

Recently, NCBI announced that due to budget constraints, it would be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. However, NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.

We now plan to continue handling sequencing data associated with:

RNA-Seq, ChIP-Seq, and epigenomic data that are submitted to GEO
Genomic and Transcriptomic assemblies that are submitted to GenBank
16S ribosomal RNA data associated with metagenomics that are submitted to GenBank

In addition, NCBI will continue to provide access to existing SRA and Trace Archive data for the foreseeable future. NCBI is also continuing to discuss with NIH Institutes approaches for handling other next-generation sequencing data associated with specific large-scale studies.

Run Browser and SRA-Instant Outage

Tue, 01 Mar 2011 14:00:00 EST

SRA is experiencing an outage to the Run Browser and SRA-Instant downloads. We are working to resolve the problems as soon as possible.

Loading and Data Availability Outage

Wed, 23 Feb 2011 12:45:00 EST

SRA is currently experiencing a temporary outage to file loading and data serving due to a hardware migration. All incoming submission files are being archived and staged as normal. Loading will resume when the hardware migration is completed.

SRA Temporary AM Outage 02/17/2011

Thu, 17 Feb 2011 12:00:00 EST

The SRA system experienced technical problems which affected both submissions to SRA and data downloads. Entrez search was not affected.
Please pardon this service interruption. All service has been restored.

NCBI To Discontinue Sequence Read Archive

Wed, 16 Feb 2011 13:00:00 EST

NCBI To Discontinue Sequence Read Archive Due to budget constraints, NCBI will be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. Closure of the databases will occur in phases. SRA and Trace will stop accepting some types of submissions in the coming weeks, and all submissions within the next 12 months. Over the next several months, NCBI will be working with staff from NIH Institutes that fund large-scale sequencing efforts to develop an approach for future access to and storage of the existing data. NCBI will continue to support and develop information resources for biological data derived from next-generation sequencing such as genotypes, common variations, rare variations, sequence assemblies and gene expression data. We therefore encourage the research community to continue submissions of these data to the applicable databases, including:     * RNA-Seq and epigenomic data to GEO
    * Variants, genotypes, phased haplotypes, and polymorphisms to dbVar, dbGaP and dbSNP
    * Genomic assemblies to GenBank/WGS
    * Transcript assemblies to GenBank/TSA
    * 16S ribosomal RNA and other targeted locus survey assemblies to GenBank NCBI expects new applications will continue to emerge for next generation technology. We are excited to work with the community to develop strategies for archiving other summary experimental measures that are informative, efficient, and valuable to the biomedical research community. For further information about submissions, contact NCBI's Help Desk.

SRA Toolkit 2.0rc5 Released

Fri, 11 Feb 2011 13:00:00 EST

An updated version of the SRA software has been released. This version includes bug fixes and performance enhancements but no new features.

SRA Toolkit 2.0rc4 Released

Sat, 05 Feb 2011 11:00:00 EST

A new release of the SRA Toolkit is now available for download. This toolkit will support the pending SRA production upgrade as well as remaining backwards compatible. Users will need to upgrade to the latest version of the toolkit to work with .sra archives generated with the updated production software.

SRA intermittent issues on 2/1/2011

Tue, 01 Feb 2011 19:00:00 EST

SRA services experienced technical problems on 2/1/2011 due to network issues at NCBI. The network problems resulted in SRA data services becoming unavailable outside of NCBI intermittently during the afternoon and evening hours.

The technical issues have been resolved and SRA services are available now. We apologize for any inconvenience this may have caused our users.

SRA Application Notes

Fri, 21 Jan 2011 12:00:00 EST

SRA has added an Application Notes section to the online documentation. These notes will address specific tools, changes, and problem fixes that are not appropriate for the standard user documenation.

SRA Bookshelf Documentation

Thu, 20 Jan 2011 11:00:00 EST

SRA documentation is now part of the NCBI Bookshelf. This will allow users to more easily find and navigate through the expanding SRA documentation. Bookshelf also includes a search function to help users find answers to specific questions.

Sequence Read Archive News Feed

Thu, 13 Jan 2011 11:00:00 EST

SRA is proud to announce an RSS feed for news related to the archive. This should allow us to make periodic updates for submitters to learn about changes, outages, and new features at SRA.