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Genomics England Research EnvironmentΒΆ


Current data release:

30th April 2024 - Workflow update

Structural Variant v3.1.1 moves to data release 18 (main-programme_v18_2023-12-21), uses default singularity cache, and uses double helix modules for nextflow version 23.10 and singularity 4.1.1

15th April 2024 - Workflow update

Small Variant v2.0.6 moves to data release 18 (main-programme_v18_2023-12-21), uses scratch for intermediate files, uses default singularity cache, uses nextflow version 22.10.5, simplifies standard output (-ansi-log false), and produces nextflow pipeline reports.

15th April 2024 - Bug in rtds table

  • There is a bug in the NCRAS radiotherapy table, rtds for 100kGP releases 17 and 18. Approximately 8% of all records in this table are missing dates. This is due to a bug translating Sep in three-letter months to numbered dates.
  • This will be fixed for release 19, due later in 2024.

15th April 2024 - Participant Explorer update

The Participant Explorer has been updated with 100,000 Genomes data release 18

14th March 2024 - GMS release 3

12th February 2024 - CloudOS access in main RE

If you are registered for CloudOS access, you can now access it from the RE desktop, and easily transfer files between CloudOS and the workspace filesystem.

7th February 2024 HPC change

We will be updating to a new HPC in spring.

15th January 2024 How to Guides

Check out the new How-to Guides section for end-to-end guides, code books and task-based tutorials.

1st November 2023 BioMart

Ensembl BioMart is now accessible in the RE, both the web interface and the biomaRt R package.

13th Oct 2023 Updated workflow

Structural Variant 3.0 is a complete re-write of the SV/CNV workflow (current version 2.0.1), from WDL/Cromwell to Nextflow DSL2. The workflow now runs in both RE (Helix/HPC) and CloudRE (CloudOS).