Program 2025
REMEMBER TO BRING A LAPTOP FOR EXERCISES
Lectures will be in person in building 303A in auditorium 44. Offline discussions will take place on Discord (https://discord.gg/7PKuKhKYQJ). 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 19th of January 2024.
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 2024
Monday, January 6
Introduction - Next Generation Sequencing
- 9:00am-9:30am
- Introduction to course (Lecture slides)
- Gabriel Renaud
- 9:30am-10:00am
- Introduction to NGS (Lecture slides)
- Gabriel Renaud
- 10:00am-10:45am
- 2nd and 3rd generation NGS Technologies (Lecture slides)
- Gabriel Renaud
- 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, Gabriel Renaud
- 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, Gabriel Renaud
- 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)
- 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 7
Data pre-processing & Alignment
- 9:00am-10:45am
- Data basics (Lecture slides) (Data basics exercise) (Data basics exercise answers)
- Gabriel Renaud, 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)
- Gabriel Renaud
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:15pm
- Alignment (Lecture slides)
- Gabriel Renaud
- 2:15pm-2:30pm
- Break
- 2:30pm-2:45pm
- Brief reminder on probabilities and Bayesian theory (Lecture slides)
- Gabriel Renaud
- 2:45pm-4:00pm
- Exercise: Alignment (Alignment exercise) (Alignment exercise answers)
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-9:30am
- Functional Human Variation
- Gabriel Renaud, (Lecture slides)
- 9:30am-10:15am
- Variant calling part 1 (Lecture slides)
- Gabriel Renaud
- 10:15am-10:30am
- Break
- 10:30am-12:00pm
- Exercise: variant calling part 1 (Postprocess exercise) (Postprocess_exercise_answers) (SNP calling exercise) (SNP_calling_exercise_answers)
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: variant calling part 2 (Lecture slides)(Handout)
- Gabriel Renaud
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: variant calling part 2 (denovo exercise) (denovo solution)
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-10:00pm
- Lecture: de novo assembly (Lecture slides)(Handout)
- Martin Sikora
- 10:00pm-10:15pm
- Break
- 10:15pm-12:00pm
- Exercise: de novo assembly (denovo exercise) (denovo solution)
- Martin Sikora, 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
- 9:00am-9:45am
- Lecture: Long read sequencing (Lecture slides)
- Frederikke Pedersen
- 9:45am-10:00am
- Break
- 10:00am-12:00am
- Exercise: Long read technology (longread exercise)(longread_exercise_answers)
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: RNAseq (Lecture slides) (Lecture slides with solutions)
- Kristoffer Vitting-Seerup
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: RNAseq (Rnaseq_exercise) (Rnaseq_exercise_answers)
- Kristoffer Vitting-Seerup, Amanda Gammelby Qvesel, Mads Hartmann
- 1:00pm-1:45pm
- Brief presentation on annotation & Recap Test (Test 2024)(answers)
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Time to work on this week's exercises
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-9:45am
- Metagenomics & Binning (Lecture slides)
- Trine Zachariasen
- 9:45am-10:00am
- Break
- 10:00am-12:00pm
- Exercise: Kaiju: Taxonomic classification (Kaiju exercise) (Kaiju solution)
- Trine Zachariasen, Cecilie Thystrup, Amanda Gammelby Qvesel
- 1:00pm-1:45pm
- Lecture: Quantitative Metagenomics (Lecture slides)
- Trine Zachariasen
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: Quantitative Metagenomics (QuantitativeMetagenomics) (QuantitativeMetagenomicsSolution)
- Trine Zachariasen, Cecilie Thystrup, Amanda Gammelby Qvesel
- 9:00am-9:55am
- Case story: Genomic Epidemiology (Lecture)
- Pimlapas Leekitecharoenphon (Shinny)
- 9:55am-10:10am
- Break
- 10:10am-12:00pm
- Exercise: Genomic Epidemiology (Genomic epidemiology exercise) (Genomic epidemiology solution)
- Gabriel Renaud
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Projects & Group formation (Lecture slides Examples from previous courses)
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 1:45pm-4:00pm
- Projects & Group formation, prepare an outline for tomorrow. please write group names in the document for 2024
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-9:45am
- Lecture: Cancer-seq (Lecture slides)
- Elena Papaleo
- 10:00am-12:00pm
- Exercise: Cancer-seq (Cancerseq_exercise) (Cancerseq_exercise_answers)
- Matteo Arnaudi, Amanda Gammelby Qvesel, Mads Hartmann
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-4:00pm
- Project consulation
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-12:00pm
- Project work
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-4:00pm
- Project work
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 10:00am-12:00pm
- Q&A: Practical information about the exam
- Project work/Office hours
- Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Written Exam
Wednesday, January 8
Alignment & Genotyping & de novo assembly
Thursday, January 9
Ancient DNA and RNAseq
Friday, January 10
Long read tech and recap test
Monday, January 13
Metagenomics
Tuesday, January 14
Genomic Epidemiology and group project
Wednesday, January 15
CancerSeq & Project work
Thursday, January 16
Project presentation
Friday, January 17
Project work
Monday, January 20
Project work
Tuesday, January 21
Project work
Wednesday, January 22
Project work
Thursday, January 23
Project Work & Produce 1 page report
Friday, January 24
Exam