Genomics England Research EnvironmentΒΆ
ANNOUNCEMENTS
Current data release:
In-person training session - 20th November
Join us for a full-day training session on using the RE in our offices in Canary Wharf.
16th July 2024 - HPC documentation
Following a consultation with our researchers, we have improved the HPC documentation, including an introduction to HPCs and detailed guidelines on running jobs.
16th July 2024 - Package update
getSVCNVperGene has been upgraded from the version 0.94 to version 2.0. This new version maintains compatibility with 100kGP data release 15 and below, while now also supporting version 16 and above. Additionally, it introduces compatibility with NHS-GMS data releases.
17th June 2024 - SACT in Participant Explorer
You can now search by cancer drug treatments and view them in medical history in Particpant Explorer
13th June 2024 - Workflow update
Small Variant v3.0.0 is a port to Nextflow DSL2 and uses Nextflow version 23.10
3rd June 2024 - Help prioritise our roadmap
You can now access our roadmap for workflows and scripts, where you can upvote existing plans and add ideas of your own.
23rd May 2024 - Workflow update
Structural Variant v3.1.2 updates bcftools to biocontainers/bcftools:1.20--h8b25389_0
- to use the latest update, edit your submission script as follows:
structural_variant='/pgen_int_data_resources/workflows/rdp_structural_variant/v3.1.2'
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,
rtdsfor 100kGP releases 17 and 18. Approximately 8% of all records in this table are missing dates. This is due to a bug translatingSepin 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
- The latest release of the Genomic Medicine Service data is now available.
- Transcriptomic data has been released for a subset of rare disease probands in the 100,000 genomes.