Program 2025
NOTE: THIS PAGE IS UNDER CONSTRUCTION WITH A NEW TEACHER IN 2026
REMEMBER TO BRING A LAPTOP FOR EXERCISES
Lectures will be in person in building 341 in auditorium 23. Offline discussions will take place on Discord (https://discord.gg/7FX35qUmGX). Please register with your full name. Will use Discord for online classes and collaboration with your project partners.
The course has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on Friday 23rd of January 2026.
For the laptop if you have a secure laptop (e.g. work laptop from Statens Serum Institut for instance), please bring your personal laptop.
Course Program - January 2025
Monday, January 5
Introduction - Next Generation Sequencing
- 9:00am-9:30am
- Introduction to course (Lecture slides)
- Mick Westbury
- 9:30am-10:00am
- Introduction to NGS (Lecture slides)
- Mick Westbury
- 10:00am-10:45am
- 2nd and 3rd generation NGS Technologies (Lecture slides)
- Mick Westbury
- 10:45am-11:00am
- Break
- 11:00am-12:00pm
- Exercise: Logging on to our pupil servers (Logging on to pupil system)
- Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann, Mick Westbury
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:30pm
- Exercise: Logging on to our pupil servers (Logging on to pupil system)
- Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann, Mick Westbury
- 1:30pm-2:15pm
- Introduction to UNIX (Video lectures to watch from "Unix intro.." to "Touching upon...") (Exercises possible answers here) (Unix Notes)
- Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann
- 2:15pm-2:30pm
- Break
- 2:30pm-3:30pm
- Introduction to UNIX (continued) (Video lectures to watch from "Unix intro.." to "Touching upon...") (Exercises possible answers here) (Unix Notes) (Intro. to UNIX pipes)
- Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann
- 3:30pm-4:00pm
- First look at data (First look exercise)
- Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann
- 3:30pm-4:00pm
- If you are done, some UNIX with zip codes (Zip codes)
- Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann
Tuesday, January 6
Data pre-processing & Alignment
- 9:00am-10:45am
- Data basics (Lecture slides) (Data basics exercise) (Data basics exercise answers)
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 10:45am-11:00am
- Break
- 11:00am-12:00pm
- Data pre-processing (Lecture slides) (Data Preprocess exercise) (Data Preprocess exercise answers)
- Mick Westbury
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:15pm
- Alignment (Lecture slides)
- Mick Westbury
- 2:15pm-2:30pm
- Break
- 2:30pm-4:00pm
- Exercise: Alignment (Alignment exercise) (Alignment exercise answers)
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-9:30am
- Functional Human Variation
- Mick Westbury, (Lecture slides)
- 9:30am-10:15am
- Variant calling part 1 (Lecture slides)
- Mick Westbury
- 10:15am-10:30am
- Break
- 10:30am-12:00pm
- Exercise: variant calling part 1 (Postprocess exercise) (Postprocess_exercise_answers) (SNP calling exercise part 1) (SNP_calling_exercise_answers part 1)
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: variant calling part 2 (Lecture slides)(Handout)
- Mick Westbury
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: variant calling part 2 (SNP calling exercise part 2) (SNP_calling_exercise_answers part 2)
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-10:00pm
- Lecture: de novo assembly and genomic annotations (Lecture slides)(Handout)
- Mick Westbury
- 10:00pm-10:15pm
- Break
- 10:15pm-12:00pm
- Exercise: de novo assembly (denovo exercise) (denovo solution)
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: RNAseq (Lecture slides)
- Kristoffer Vitting-Seerup
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: RNAseq (Rnaseq_exercise)
- Kristoffer Vitting-Seerup, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-10:00pm
- Ancient DNA (Lecture slides)
- Martin Sikora
- 10:00pm-10:15pm
- Break
- 10:15pm-12:00pm
- Exercise: Ancient DNA (Ancient DNA exercise) (Ancient_DNA_exercise_answers)
- Martin Sikora, Amanda Gammelby Qvesel, Mads Hartmann
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:00pm
- Lecture: 3D Genomics with Hi-C (Lecture slides)
- Juan Rodríguez
- 2:00am-2:15pm
- Break
- 2:15pm-4:00pm
- Exercise: 3D Genomics with Hi-C (longread exercise)(longread_exercise_answers)
- Juan Rodríguez, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-9:45am
- TBA (Lecture slides)
- Rasmus Lykke Marvig
- 9:45am-10:00am
- Break
- 10:00am-12:00pm
- Exercise: TBA (Kaiju exercise) (Kaiju solution)
- Rasmus Lykke Marvig, Amanda Gammelby Qvesel, Mads Hartmann
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: TBA (Lecture slides)
- Rasmus Lykke Marvig
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: TBA (QuantitativeMetagenomics) (QuantitativeMetagenomicsSolution)
- Rasmus Lykke Marvig, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-9:55am
- TBA (Lecture)
- David Duchene
- 9:55am-10:10am
- Break
- 10:10am-12:00pm
- Exercise: TBA (Genomic epidemiology exercise) (Genomic epidemiology solution)
- David Duchene
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: TBA (Lecture slides)
- David Duchene
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: TBA (QuantitativeMetagenomics) (QuantitativeMetagenomicsSolution)
- David Duchene, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-9:55am
- TBA (Lecture)
- Luke Holman
- 9:55am-10:10am
- Break
- 10:10am-12:00pm
- Exercise: TBA (Genomic epidemiology exercise) (Genomic epidemiology solution)
- Luke Holman
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:30pm
- Recap Test (Test 2025)(answers)
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 1:30pm-1:45pm
- Break
- 1:45pm-2:30pm
- Projects & Group formation (Lecture slides Examples from previous courses)
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 2:30pm-4:00pm
- Projects & Group formation, prepare an outline for tomorrow. please write group names in the document for 2025
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-12:00pm
- Project work
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-4:00pm
- Project work
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 10:00am-12:00pm
- Q&A: Practical information about the exam
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Written Exam
Wednesday, January 7
Variant calling
Thursday, January 8
Assembly, annotation and RNA-seq
Friday, January 9
Ancient DNA and 3D genomics
Monday, January 12
Microbial genomics
Tuesday, January 13
Phylogenomics
Wednesday, January 14
Metabarcoding and group project
Thursday, January 15
Project presentation
Friday, January 16
Project work
Monday, January 19
Project work
Tuesday, January 20
Project work
Wednesday, January 21
Project work
Thursday, January 22
Project Work & Produce poster
Friday, January 23
Exam