14th – 15th January 2021
Together with the ARTIC network, we organised a two-day workshop about COVID-19 data analysis. All the information related to the workshop is shared on this page, including the recordings.
“Theory” (live sessions) and “practice” (homework) are separate, so everyone will be able to choose what to take or to do from this course at their own pace.
Slack
We created a Slack workspace for chat and questions. Although it was initially thought to be used by participants only, we appreciate it might be useful for others too. We need to make sure the Slack channel is properly used and looked after; please, fill this form to request access.
Programme with links to recordings
Talks
- Introduction (Nick Loman)
- Why do genomic epidemiology? (Sam Sheppard)
- How to sequence COVID-19 using the ARTIC protocol (Josh Quick)
- ARTIC Nanopore Bioinformatics Pipeline (Will Rowe)
- ARTIC Nanopore+Illumina Nextflow Pipeline (Matt Bull)
- Bioinformatics “gotchas” (Nabil-Fareed Alikhan)
- Introduction to genomic epidemiology of COVID-19 (Verity Hill)
- Practical phylogenetics: lineages & variants (Aine O’Toole)
- Getting started (lab-on-SSD, CLIMB and Virtual Box) and introduction to homework (Nick Loman) – Homework assignments are listed here below
- Review of homework (chair: Nick Loman)
- Panel discussion and morning Q/A session (chair: Nick Loman)
- Afternoon Q/A session (chair: Nick Loman)
- Microbial genomics and bioinformatics: progress and perspectives & Concluding Remarks (Mark Pallen)
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
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/pangolin_tutorial.html
Genomic Epidemiology with Civet by Verity Hill
- Homework: https://drive.google.com/file/d/1a4Gl64PdbpdFB_6c53pv4EQSUnu0Ftjs/view?usp=sharing
- Input data file and config: https://artic.s3.climb.ac.uk/input-data.zip
- Background data file: https://artic.s3.climb.ac.uk/background_data-final.zip
- Example report (if you can’t run Civet): https://artic.s3.climb.ac.uk/civet-example-output.zip
Installing Bioconda by Bioconda
- Homework link: https://bioconda.github.io/user/install.html
Installing Lab-on-SSD by Radoslaw Poplawski
