Virtual Workshop – 13-14 January 2022

Programme and Recordings:

The third joint ARTICnetwork and CLIMB-BIG-DATA workshop on COVID-19 data analysis was held on 13-14 January 2022. We focused on a mixture of talks, panel discussions, practical hands-on, and questions & answers sessions.

DAY 1: THURSDAY, 13 JANUARY 2022

Introduction to the ARTIC&CLIMB-BIG-DATA workshop and the ARTIC project (Nick Loman)

Case studies in molecular epidemiology of SARS-CoV-2 (Andrew Page)

How to sequence COVID-19 using the ARTIC protocol (Josh Quick)

Automating the ARTIC protocol using the OpenTrons OT2 (Jeremy Mirza)

ARTIC Nanopore+Illumina Bioinformatics Pipeline (Sam Wilkinson)

Bioinformatics “gotchas” (Nabil-Fareed Alikhan)

DNA Spike-Ins for SARS-CoV-2 sequencing (Katherine Siddle)

Wastewater sequencing bioinformatics (Chris Quince)

Discussion, homework setting and finish (Nick Loman)

DAY 2: FRIDAY, 14 JANUARY 2022

A practical introduction to phylogenetics in the pandemic era (JT McCrone)

Practical phylogenetics: lineages & variants (Rachel Colquhoun)

How we detect and define new variants (Natalie Groves)

Panel discussion (chaired by Nick Loman)

Homework Assignments

Each homework assignment is standalone. There are questions to work through at the end.

Primal Scheme by Josh Quick

• Homework link: https://docs.google.com/document/d/17-n3bAmOao4mFoqaD5lnJbZb1C_3l-XJ7bFg4Pn0bgg/edit?usp=sharing

ARTIC Bioinformatics Pipeline by Will Rowe

• Homework link: https://mybinder.org/v2/gh/will-rowe/artic-pipeline-example/main?filepath=notebooks/artic_pipeline_example.ipynb
• Download presentation PDF.

Bioinformatics Gotchas by Nabil-Fareed Alikhan

• Homework link: https://docs.google.com/document/d/1dfKTftER00WAFUcv_jzDYBDJ81WJceP6oc25nWXFIow/edit#heading=h.9q107s61hk0h

Assigning Lineages with Pangolin by Aine O’Toole

• Homework link: https://cov-lineages.org/resources/pangolin/tutorial.html

Installing Bioconda by Bioconda

• Homework link: https://bioconda.github.io/user/install.html

Installing Lab-on-SSD by Radoslaw Poplawski

• Homework link: https://docs.google.com/document/d/1BVPV-DHGVUWX_2Dmzx6i5QXMLfwZdro4ixxJ4oSQnu8/edit#

Civet by Aine O’Toole

https://s3.climb.ac.uk/artic/background_data.zip

https://s3.climb.ac.uk/artic/config.yaml