Data access

Q. How far has my species of interest progressed and when will data be released?

• A. You can check the status of the species in the DToL portal at https://portal.darwintreeoflife.org/tracking. This provides progress tracking from registering of the sample through to the annotation being completed. For a more detailed view of the data generated (in case there is any already) check ToLQC at https://tolqc.cog.sanger.ac.uk/ where you will also find links to any released raw data. If your species of interest has had an assembly built and it has been released to the public archives and possibly also already annotated and a genome note being published, the portal will link to the relevant sources. Whilst many species take about 6-9 months to go through the pipeline from extraction to release, we can’t guarantee a certain time period as every species comes with its unique challenges.

Q. Can I have early access to intermediate assemblies of species X?

• A. Whilst this creates quite an overhead, it is certainly possible. Please check the current status of your species of interest (see above) and if there is no assembly released yet, but having any assembly data is essential for your science, please request an intermediate release via contact@darwintreeoflife.org. Be aware that it will be of inferior quality and likely to change substantially on release.

Q. We are working on a project with a certain species and need the data/assembly urgently, what can we do to speed it up?

• A. Please contact contact@darwintreeoflife.org to describe your case. Our project management will aim to prioritize your species of interest, if that is possible and resources are available. Even if it is prioritized, we can not guarantee it will be completed rapidly – various technical issues can cause indefinite delays.

Q. Where can I ‘browse’ along a Darwin Tree of Life genome assembly?

• A. Annotated DToL genomes can be browsed through the Ensembl Genome Browser, via our Rapid Release website. The easiest way to access the data is to use our Ensembl DToL Project Page. From here use the “View in browser column” to open your species of interest in the Ensembl Genome Browser.

Q. Where can I do a ‘BLAST’ search against a Darwin Tree of Life genome assembly?

• A. You can BLAST against a genome of interest for any genome released in the Ensembl Genome Browser. On our Rapid Release website, you can access BLAST via the banner at the top of any page. This will allow you to select one or more species to include in the BLAST session. You may BLAST against either the genomes or the proteomes/