ARTICnetwork and CLIMB-BIG-DATA Joint Workshop

14-15 July 2021

Together with the ARTIC network, we organised the 2nd two-day workshop about COVID-19 data analysis.

“Theory” (live sessions) and “practice” (homework) were separate, so everyone was able to choose what to take or to do from this course at their own pace.

Should you need any information, please drop an email to Lisa.Marchioretto@quadram.ac.uk.

Programme and Recordings

How and why sequence SARS-CoV-2?

Day 1 – Wednesday 14th July 2021

Introduction to the ARTIC-CLIMB 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)
ARTIC Nanopore Bioinformatics Pipeline (Will Rowe)
ARTIC Nanopore+Illumina Nextflow Pipeline (Matt Bull)
Q&A (chaired by Nick Loman)

SARS-CoV-2 sequence quality control and ncov-qc (Jared Simpson)
Bioinformatics “gotchas” (Nabil-Fareed Alikhan)
Wastewater sequencing bioinformatics (Chris Quince) – Recordings not available (unpublished data)
Discussion

Day 2 – Thursday 15th July 2021

Introduction to genomic epidemiology of COVID-19 (Verity Hill)
Practical phylogenetics: lineages & variants (Aine O’Toole)
How we detect and define new variants (Natalie Groves)
Q/A, Panel discussion and close

Homework Assignments

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

Primal Scheme by Josh Quick

ARTIC Bioinformatics Pipeline by Will Rowe

Bioinformatics Gotchas by Nabil-Fareed Alikhan

Assigning Lineages with Pangolin by Aine O’Toole

Installing Bioconda by Bioconda

Installing Lab-on-SSD by Radoslaw Poplawski

Civet by Aine O’Toole

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

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