Changes to WGS and TSA sequences in the ENA browser

ENA is making some improvements to the handling of WGS and TSA sequence in the ENA browser, with the main focus on treating them as whole sets rather than individual sequences. These changes are being made to both address the very large increase of WGS set submissions we have seen in the last 12 months, but also to make WGS sets more usable to consumers. Note that for the purposes of this announcement, the TSA sequences that we are referring to are only those that have been submitted as part of a set (these all have a four letter prefix). There is no change to TSA sequences submitted before this set-based submission was introduced.

Individual sequences will still be available from the ENA browser via their accession number, e.g.
http://www.ebi.ac.uk/ena/data/view/CBMM010000001

Using the individual sequence accession from the text search box at the top of any ENA page will also result in the individual record page such as the example above. However, any text search from the main EBI page using an individual sequence accession will result in you finding the master record for the set, rather than the individual sequence, from where you will be able to reach each individual sequence or download the set as a whole. This has already been changed for WGS sequences and will soon be rolled out to TSA sequences.  This will also affect any EBI or ENA text search based on non-accession terms (e.g. "human"), which will return the master record only.

All master records (describing the set) are available using the accession pattern LLLLVV000000, where LLLL is the four letter prefix and VV is the build number, e.g.: http://www.ebi.ac.uk/ena/data/view/CEDP01000000
Note that while individual sequence accessions have a variable length based on when they were submitted and how big the set was, master accessions will always have only 6 zeros after the build number.

There is not yet a direct link from the master record page to download the WGS set, however there is a link to the range of sequences in the set from the Navigation tab. From the resulting page, you can download the full set, or the desired range of sequences, in your choice of TEXT (flat file), FASTA or XML formats, e.g.:
http://www.ebi.ac.uk/ena/data/view/CEDP01000001-CEDP01000100

WGS and TSA masters have now been added to Advanced search, and can be searched under the new "Contig set" domain. The results for these are "wgs_set" and "tsa_set" respectively. Using the normal advanced search display/download options, you will only obtain the master record. You can however download a report listing the FTP file location of the set for your search result and including "set_files" in the list of fields to be included in the report, e.g.:
http://www.ebi.ac.uk/ena/data/warehouse/search?query=%22tax_eq(9606)%22&result=wgs_set&display=report&fields=set_files
The report is produced in a tab separated format and if there are multiple files for a single set, these are presented as a semi-colon delimited list. This report can then be processed in a script to download each of the files from your search via wget or curl.

Currently, individual WGS and TSA sequences are still included within the "Sequence" domain ("sequence_release" and "sequence_update" results). From Monday 7th March, we will be removing the individual WGS and TSA sequences from this domain:

1. On 7th March, WGS and TSA sequences will no longer be included in the "sequence_update" result.
2. The "sequence_release" result will be updated when the next release is available, approximately 2 weeks later. At this point, the WGS and TSA sequences will only be available via the "Contig set" domain.