COG-UK Docs
View the Project on GitHub
COG-UK/docs
Majora and CLIMB-COVID user accounts
How to register for Majora and CLIMB-COVID accounts
Acceptable Use Policy for CLIMB-COVID
Uploading sequences
How to upload sequences to CLIMB
Uploading metadata
Basic terminology and minimal requirements
You think you are ready to submit metadata?
How to upload metadata to CLIMB with the metadata uploader
Easy explainer for biosample metadata fields
Uploading a library and sequencing run without the biosample
API documentation for developers and advanced users
Quality control and post-processing
What quality control is done on data uploaded to CLIMB?
Geographical metadata cleaning information
Accessing data on CLIMB-COVID
Setting up Ocarina and OAuth
Generating a legacy API key in Majora
What is the timeline for the automated CLIMB pipelines?
How to access data stored on CLIMB
How to access a dataview using the API (Ocarina)
Analysing data and submitting jobs on CLIMB
Data changelog
Data integrity incidents
Fixing bad data
Suppressing a sequence from the COG data set
Meta-metadata
Cycle threshold validators
Validating a centrally assigned Heron barcode
Outbound distribution
Automated GISAID submissions FAQ
Automated ENA consensus submissions FAQ
ENA Bioproject PRJEB37886
Public accessions interface
Infrastructure
Authorising applications to use your Majora account using OAuth
Registering and using an OAuth application
Joining and using the interpipeline communucation network
CLIMB-COVID Status
Lab protocols
COG-UK sequencing protocols group on Protocols.io
WSI COVID-19 ARTIC v3 Illumina library construction and sequencing protocol (version:bgq3jvyn)
Bioinformatics pipelines
Nextflow workflows for amplicon Illumina and nanopore
CoV-GLUE
Accessing CoV-GLUE on CLIMB
Reporting primer and probe mismatches using CoV-GLUE
Misc
Slack channel new-user reference
Adding a page to this site