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Wastewater sequencing bioinformatics (Chris Quince) – Recordings not available (unpublished data)
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
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