News


12 Sep 2013	ENA release 117 Release 117 of assembled/annotated sequences from the European Nucleotide Archive (ENA) is now available on the EBI public ftp server at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/. It contains 324,201,244 sequences comprising 670,004,320,378 nucleotides. You can see the full release notes at: http://bit.ly/LKFtrE. ENA captures, preserves and presents the world's nucleotide sequence data. New content is included in ENA on a continuous basis and are distributed daily from our browser and RESTful service. The ENA assembled/annotated sequence release provides a quarterly snapshot of content in this important subset of ENA content.
2 Jul 2013	Change to EMBL-Bank flat file AC lines Use of AC lines to denote 'WGS/TSA set membership' in addition to 'record replacement' has been a frequent cause of confusion among our users. To solve this we have moved WGS/TSA master accession numbers from AC lines to DR lines. E.g.: Before the change: AC CAJV010000001; CAJV010000000; CAJV000000000; After the change: AC CAJV010000001; DR ENA; CAJV010000000; SET. DR ENA; CAJV000000000; SET. The DR line format is: DR ENA; <WGS/TSA master accession number with set version>; SET DR ENA; <WGS/TSA master accession number without set version>; SET If you have any questions please do not hesitate to contact us at datasubs@ebi.ac.uk.
27 Jun 2013	ENA release 116 Release 116 of assembled/annotated sequences from the European Nucleotide Archive (ENA ) is now available on the EBI public ftp server at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/. It contains 309,513,621 sequences comprising 616,248,681,624 nucleotides. You can see the full release notes at: http://bit.ly/LKFtrE. ENA captures, preserves and presents the world's nucleotide sequence data. New content is included in ENA on a continuous basis and are distributed daily from our browser and RESTful service. The ENA assembled/annotated sequence release provides a quarterly snapshot of content in this important subset of ENA content.
13 Jun 2013	CRAM 2.0 launch The CRAM 2.0 release is now available, comprising our sequence data compression format, its supporting software toolkits and the CRAM reference registry. CRAM 2.0 release follows a two-month period of community feedback and include numerous improvements over CRAM 1.0, which is now superseded. More information about CRAM can be found here.
26 Mar 2013	CRAM 2.0 pre-launch CRAM 2.0 release candidate made available and two month review period announced. Today sees the pre-launch of CRAM 2.0 and an announcement of the expected full launch date as the 1st of June, 2013. This pre-launch comprises the publication of a release candidate for CRAM 2.0, our sequence data compression format, its supporting software toolkit and the CRAM reference registry. CRAM 2.0 contains numerous improvements over CRAM 1.0 made possible by active community participation. Minor modifications to the format are possible during the two month review period that now begins. CRAM 1.0 will be superseded by CRAM 2.0 at time of full launch. More information about CRAM can be found here.
13 Feb 2013	Changes to EMBL-CDS FTP products The introduction of ENA Advanced Search and other recent service improvements have made a number of EMBL-CDS FTP products redundant. Any remaining users are asked to contact datasubs@ebi.ac.uk to discuss alternative ways to retrieve this information. If you have any questions please do not hesitate to contact datasubs@ebi.ac.uk. Changes to EMBL-CDS flat file format Removal of CRC32 checksum from SQ lines. After this change the EMBL-CDS flat file SQ line will be identical to EMBL-Bank flat file SQ line. Removal of OX line. Please use /db_xref="taxon:" in the source feature instead as in EMBL-Bank flat files. Removal of /func_charaterized qualifier. Changes to EMBL-CDS FTP reports The following reports will be discontinued. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/numbers.txt This file contains the number of protein_ids and the number of unique CRC32 checksums, for example: protein_ids# crc32# ------------ -------- 41700210 29242014 ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/README.txt The README file explains the reports in the directory. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/by_exon.gr.gz A grouping by shared exons. For example: ID A00033.1:1..1155 CAA00001 // ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/by_gene.gr.gz A grouping by gene name. For example: ID 00011b03 CAR63565 // ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/by_inference.gr.gz A grouping by /inference qualifier. For example: ID alignment:clustalx:2.0:insd\|p29289.1, insd\|p29290.1,insd\|p29291.1 ACS36539 ACS36540 // ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/by_species.gr.gz A grouping by organism name, as seen in the OS line of the entry. For example: ID 'Azulnota' sp. 'punctana' AEZ87687 AEZ87688 // ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_characterised.lis.gz List of CDS accession numbers extracted from the non-wgs section of the database where /func_characterised qualifier is present. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_complete.lis.gz List of CDS accession numbers extracted from the non-wgs section of the database where the CDS sequence is complete. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_experimental.lis.gz List of CDS accession numbers extracted from the non-wgs section of the database where /experiment qualifiers is present. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_wgs_characterised.lis.gz List of CDS accession numbers extracted from the wgs section of the database where /func_characterised qualifier is present. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_wgs_complete.lis.gz List of CDS accession numbers extracted from the wgs section of the database where the CDS sequence is complete. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_wgs_experimental.lis.gz List of CDS accession numbers extracted from the non-wgs section of the database where /experiment qualifiers is present. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_wgs_withNs.lis.gz List of CDS accession numbers extracted from the wgs section which contains at least one completely ambiguous codon. ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/lists/cds_withNs.lis.gz List of CDS accession numbers extracted from the non-wgs section which contains at least one completely ambiguous codon.
20 Nov 2012	CRAM launches... Today sees the launch of the CRAM compression software and format. CRAM provides not only powerful compression through its lossless and lossy models, but also supports full computational access to data in compressed form. See the full news item here and find out more about CRAM here.
9 Nov 2012	RESTful and Query builder interfaces to ENA launched in beta New tools to discover and retrieve the world’s nucleotide sequence data have been launched today, in early beta, based on a new custom data warehouse that brings together the diverse content of ENA. The Query builder function, a web interface for the construction of powerful queries, provides interactive access, while the RESTful interface supports programmatic calls to the warehouse. The Query builder is available from the ‘Advanced search’ tab on any search results page and is documented, along with the RESTful interface here. These two interfaces will in due course be complemented with a third warehouse-based search interface that offers more intuitive access with much of the search power. We encourage users to send feedback on this and other ENA services to datasubs@ebi.ac.uk.
3 Aug 2012	Approaching full production for CRAM Since our proof-of-principle publication of reference-based sequence read data compression in 2011 (http://genome.cshlp.org/content/21/5/734), the EBI has been moving towards a production release of CRAM, a framework technology comprising file format and toolkit in which we combine highly efficient and tunable compression with a data format that is directly available for computational use (http://www.ebi.ac.uk/ena/about/cram_toolkit). Details of our plans are provided here.
13 Jul 2012	Just published: 'The future of DNA sequence archiving' Our latest paper has been published in the inaugural issue of Gigascience. In this commentary, our starting point is the existence of a viable compression method, CRAM - currently in late beta and soon to be released in full production - in which compression can be applied with varying levels of intensity to different data sets. Our goal with the paper is to stimulate the broadest possible community discussion about exactly where the most aggressive forms of compression should be applied and where the approach should be far more cautious.
25 Apr 2012	CRAM 0.8 released CRAM toolkit 0.8 has been released. More information with download, installation and usage instructions are available here.
25 Apr 2012	ENA policy relating to compression of submitted data ENA details its policy on use of CRAM raw sequence data compression during the archiving process.
7 Mar 2012	CRAM toolkit 0.7 released CRAM toolkit 0.7 has been released. More information with download, installation and usage instructions are available here.
2 Mar 2012	The future of sequence archiving The future of sequence archiving and the role of data compression is explored in a new paper from EBI to be published in Gigascience. Planned for the first issue of the journal, the paper is available pre-publication here. In the paper, we propose a way forward through the use a graded system in which the ease of reproduction of a sequencing-based experiment and the relative availability of a sample for resequencing be used as a means to define the level of lossy compression to apply to the stored data.
13 Feb 2012	CRAM toolkit 0.6 released CRAM toolkit version 0.6 has been released. More information with download, installation and usage instructions are available here.
20 Jan 2012	ENA training videos now available on the EMBL-EBI YouTube Channel Train yourself on Sequence Read Archive submissions theory and practice with ENA training videos now uploaded to the EMBL-EBI YouTube Channel for simpler access. We believe that such videos are useful additions to our support services and plan to cover more areas of ENA as time goes by. Contact us at datasubs@ebi.ac.uk with suggestions of ENA services that you would like to see covered.
6 Jan 2012	ENA data go Galactic Next generation sequence data from ENA's Sequence Read Archive (SRA) are now available as a data source in the Galaxy analysis system. SRA data can be browsed and selected for upload using the Galaxy 'Get Data' tool. The 'EBI SRA' data source forwards users to ENA's pages to upload data into Galaxy. In ENA, links are provided to Galaxy that upload data into the system and launch a session. For example, the following URL provides a list of all fastq files associated with SRA study ERP000591: http://www.ebi.ac.uk/ena/data/view/ERP000591. The Galaxy file upload links are available in the column 'Galaxy'.
4 Nov 2011	CRAM toolkit 0.5 released CRAM toolkit version 0.5 has been released with support for several new quality budget models, random access index, and support for the Picard API. More information with download, installation and usage instructions are available here.
3 Aug 2011	CRAM toolkit 0.3 released CRAM toolkit version 0.3 has been released with support for read quality masking (selective preservation of base quality scores). More information with download, installation and usage instructions are available here.
16 Mar 2011	ArchiveBAM 1.0 specification The ArchiveBAM 1.0 specification has been published. SRA submitters are adviced to submit their data using the BAM format. The specification is available here.
11 Mar 2011	ENA User Survey 2011 now available Have your say and help us to improve ENA in our brief survey at http://www.surveymonkey.com/s/ENA_User_Survey_2011.
7 Mar 2011	Next Generation Sequencing Workshop at EBI Spaces still available on the SRA user course: EBI Affiliated Course - Next Generation Sequencing Workshop 2011. The course will take place at EBI on the 4th-6th April 2011. Further details are available here.
26 Jan 2011	EMBL-EBI and Sequence Read Archive EMBL-EBI will continue to support the Sequence Read Archive for raw data. See here for further details.
6 Dec 2010	MIENS specification The MIENS specification for describing marker genes was published in Nature Precedings. The full article is available here.
9 Nov 2010	SRA article An article describing the Sequence Read Archive (SRA) services was published in the Nucleic Acids Research 2011 Database Issue. The full article is available here.
23 Oct 2010	ENA article An article describing the European Nucleotide Archive (ENA) services was published in the Nucleic Acids Research 2011 Database Issue. The full article is available here.

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