Changes to read data submission services 1st of October 2015

ENA will make a number of changes to submission services for raw sequence read data on first of October 2015. We continue to track an ever evolving landscape of available and preferred formats and introduce these changes with a view to overall simplification of the submission system to allow us to provide a more efficient service with faster turnaround.

We will continue to recommend submission of reference-aligned data: First, we strongly recommend submission in the preferred format, CRAM. The CRAM format assures the tightest integration with the various downstream services that ENA offers and provides for the greatest data discoverability and most flexible retrieval options. Second, we will continue to accept data in BAM format and recommend strongly that the reference accession(s) that have been used for aligned reads in this format are explicitly declared using database accessions from INSDC. We also support read submissions in PacBio, Oxford Nanopore, and Complete Genomics native formats as well as SFF format (e.g. 454 and Ion Torrent). We will cease to support new submissions in SRF, SOLID native, SOLID CSFASTA, and Ilumina QSEQ formats. These correspond to the SOLID_NATIVE, ILLUMINA_NATIVE, ILLUMINA_NATIVE_QSEQ, ILLUMINA_NATIVE_FASTQ, SOLID_NATIVE_CSFASTA, SOLID_NATIVE_QUAL, SRF file types in the SRA XML.

While Fastq submissions continue to be accepted where the usage of the format complies with ENA requirements, we encourage all submitters to transition to CRAM (noting that unaligned reads can also be represented in CRAM format when necessary). Full details of our Fastq format requirements are available at http://www.ebi.ac.uk/ena/submit/read-file-formats#fastq_format. Our Fastq usage requirements cover the major usages of the format and include data currently submitted from the vast majority of submitters, platforms and analytical software tools.

Read data submitted from first of October 2015 that fail to comply with our format requirements may be rejected. In this case, submitters will be informed and encouraged to re-submit the data in another format. In typical cases, read data can be re-resubmitted without needing to provide for a second time details of the study, sample and experimental configuration information.

We encourage users to contact datasubs@ebi.ac.uk for any queries relating to these changes.