Welcome to populationgenomics’s documentation!

Welcome to the Centre for Population Genomics! We’re glad to have you here :)

This repository contains documentation you might find useful as you onboard, but and as an ongoing reference. We sometimes let these docs fall out of date, so please have a chat on Slack if something seems unclear - or open a pull request!

If you need help more urgently, don’t hesitate to ask directly on Slack (e.g. in the #team-data or #software-questions channels).

Where to next?

• If you’re new to the centre, check out the Welcome to the CPG guide.

• If you’re looking for help, check out Getting help at the CPG.

• Want to learn more about infrastructure? Start at: CPG Infrastructure.

About the centre

• Reproducible analyses
• Storage policies

Libraries

• cpg-utils
• Production Pipelines
• Metamist

Infrastructure

• CPG Infrastructure
• CPG Infrastructure User Guide
• CPG Infrastructure Developer Guide

Guides

• Notebooks
• Setting up a new repository
• Style guide for R
• Configuration
• Data Sharing
• Budgets
• IGV
• Docker Images
• Kubernetes cheatsheet

Playbooks

• Hail: Batch playbook
• Hail: Query on Batch Playbook
• Hail: Query on Dataproc Playbook

Indices and tables

• Index

• Module Index

• Search Page