CLIMB-TRE¶
Introduction¶
The CLIMB Trusted Research Environment (CLIMB-TRE) project provides tools with which users can upload metagenomics data, with metadata, and analyse them on CLIMB.
This site documents how to use the CLIMB-TRE tools and is distinct from more general documentation on using CLIMB. Read further for general information on how to upload or analyse data.
Contents¶
Getting Started¶
How to Upload Data
Learn how to upload data to CLIMB-TRE.
Checking Submission Results
Learn how to check the status of data submitted to CLIMB-TRE.
Analysing Data
Get started analysing data within CLIMB-TRE using Onyx.
Further Examples
Further project-specific analysis examples using Onyx.
Project Specifications¶
Common Structure
Learn more about required files, naming conventions and processing requirements common to all projects.
Project List¶
| Project | Description | Uploader Specification | Analysis Specification | Template CSV |
|---|---|---|---|---|
| mSCAPE | Metagenomics Surveillance Collaboration and Analysis Programme | Uploader Specification | Analysis Specification | mscape-template.csv |
| PATH-SAFE | Pathogen Surveillance in Agriculture, Food and Environment | Uploader Specification | Analysis Specification | pathsafe-template.csv |
| synthSCAPE | Synthetic dataset for mSCAPE | Uploader Specification | Analysis Specification | synthscape-template.csv |
| openMGS | Open Meta-Genomic Surveillance | Uploader Specification | Analysis Specification | openmgs-template.csv |