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