SARS-CoV-2 Bioinformatics & Data Science

A practical introduction to genomic surveillance using SARS-CoV-2 as an example and in the context of the FU course "SARS-CoV-2 Bioinformatics & Data Science" 2024.

Schedule links for the workshop

• 2024-09-23 - Monday: Welcome, Linux re-cap, container, WMS
• 2024-09-24 - Tuesday: SARS-CoV-2 sequencing & genome reconstruction
• 2024-09-25 - Wednesday: SARS-CoV-2 evolution, mutation profiling & phenotypization
• 2024-09-26 - Thursday: SARS-CoV-2 pathogen evolution & genome-based incidence estimation
• 2024-09-27 - Friday: SARS-CoV-2 phylogeny & outbreak investigation

Instructors

• Max von Kleist (FU, RKI) and Martin Hoelzer (RKI) & many great colleagues

Schedule

All events are held at FU Arnimallee 6, Room 017

Monday, 2024-09-23

Time	Welcome, Linux re-cap, container & WMS
10:00-10:30	Welcome & course intro
10:30-11:00	RKI Genomic Surveillance and SARS-CoV-2
11:00-12:00	Linux re-cap
12:00-13:00	Lunch break
13:00-14:00	Container & WMS
14:00-14:30	Coffee break
14:30-16:00	Hands-on & demo
16:00-16:15	Wrap-up & questions

Tuesday, 2024-09-24

Time	SARS-CoV-2 sequencing & genome reconstruction
10:00-10:15	Debriefing previous day
10:15-11:00	Sequencing (SARS-CoV-2)
11:00-12:00	SARS-CoV-2 genome reconstruction
12:00-13:00	Lunch break
13:00-14:30	Hands-on & demo
14:30-15:00	Coffee break
15:00-15:45	Continue practical session
15:45-16:00	Wrap-up & questions

Wednesday, 2024-09-25

Time	SARS-CoV-2 evolution, mutation profiling & phenotypization
10:00-10:15	Debriefing previous day
10:15-11:00	SARS-CoV-2 genome organisation & evolution
11:00-12:00	SARS-CoV-2 epistasis and variants
12:00-13:00	Lunch break
13:00-14:00	SARS-CoV-2 nomenclature
14:00-14:30	SARS-CoV-2 mutation profiling
14:30-15:00	Coffee break
15:00-15:45	Hands-on & demo
15:45-16:00	Wrap-up & questions

Thursday, 2024-09-26

Time	SARS-CoV-2 pathogen evolution & incidence estimation
10:00-10:15	Debriefing previous day
10:15-10:45	SARS-CoV-2 Variant prioritization via VOCAL
10:45-11:15	SARS-CoV-2 Evolution on a Dynamic Immune Landscape
11:15-11:45	Hands-on (SARS-CoV-2 Evolution on a Dynamic Immune Landscape)
12:00-13:00	Lunch break
13:00-14:00	SARS-CoV-2 pathogen evolution and genome-based incidence estimation
14:00-14:30	Coffee break
14:30-15:45	Hands-on & demo
15:45-16:00	Wrap-up & questions

Friday, 2024-09-27

Time	SARS-CoV-2 phylogeny & outbreak investigation
10:00-10:15	Debriefing previous day
10:15-12:00	Phylogeny and outbreak investigation
12:00-13:00	Lunch break
13:00-14:00	Outbreak detection & clustering via breakfast
14:00-14:30	Coffee break
14:30-15:45	Hands-on & demo
15:45-16:00	Wrap-up & questions

Project work 2024-09-28 to 2024-10-03

Friday, 2024-10-04

Time	Project presentations
10:00-11:00	Project I
11:00-12:00	Project II
12:00-13:00	Lunch break
13:00-14:00	Project III
14:00-15:00	Project IV
15:00-16:00	Project V
15:00-15:15	Wrap-up

Acknowledgement

This course material is partly based on the following resources and on contributions from great people (no specific order):

• Martin Hoelzer, RKI MF1, content about Linux, container, Nextflow, sequencing, genomic surveillance & glueing everything together
• Sebastian "Raverjay" Krautwurst, FSU Jena, some Linux and ONT content
• Stephan Fuchs, RKI MF1, some Linux and Assembly content
• Matt Huska, RKI MF1, automatic test script for all md code blocks using codedown and general help
• Workshop structure inspired by https://github.com/cinemaparis/2023
• Max von Kleist, RKI P5 and FU Berlin, basically most content about sequencing and SC2 data science (evolution, epistasis, incidence esitmation, ...)
• Maureen Smith, Maria Trofimova, RKI P5 and FU Berlin, content on Incidence estimation
• Hugues Richard, RKI MF1, content about SC2 risk assessment
• Matt Huska & Denis Beslic, RKI MF1, content about SC2 outbreak detection & clustering
• We thank the GISAID initiative for providing a framework for sharing SARS-CoV-2 sequence data internationally and all the submitting labs