Genomics England Research Environment

ANNOUNCEMENTS

Current data release:

• /main-programme/main-programme_v17_2023-03-30
• nhs-gms/nhs-gms-release_v2_2023-02-28

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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).

14th September 2023 - Update to AggV2 functional annotation data

• We are pleased to announce that updated functional annotation files have been made available for the AggV2 dataset using VEP 109. For more information on this data, please see https://re-docs.genomicsengland.co.uk/functional_annotation/ and, as always, please do get in touch via the Service Desk if you have any questions.

2nd June 2023 - R packages in the AWS Research Environment

• Following the transition to AWS, we encourage you to create and maintain your own personal R package libraries. See Self-service R package installation in the Research Environment for more details.

12th May 2023 - Cloud-RE documentation

• Documentation for the Cloud-RE has moved location. Documentation describing the CloudOS platform and its functionality is now hosted by LifeBit, while documentation describing the Genomics England data within the Cloud-RE can be found within these pages.

3rd May 2023 - Updated workflow

• Small Variant 2.0 is a complete re-write of the Gene variant workflow (current version 1.7), from WDL/Cromwell to Nextflow DSL1. The workflow now runs in both RE (Helix/HPC) and CloudRE (CloudOS).

Getting started

Data in the Research
Environment

Tools in the Research
Environment

High Performance
Cluster (HPC)

Pre-made scripts and
workflows for data analysis

Getting help

Data security and you

Tutorials

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Last update: November 17, 2023