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/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 24th of January 2025.

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

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Monday, January 6

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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)

(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

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Tuesday, January 7

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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

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Wednesday, January 8

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Variant calling

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

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Thursday, January 9

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Assembly, annotation and long read sequencing

9:00am-10:00pm

Lecture: de novo assembly and genomic annotations (Lecture slides)(Handout)

Gabriel Renaud

10:00pm-10:15pm

Break

10:15pm-12:00pm

Exercise: de novo assembly (denovo exercise) (denovo solution)

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

12:00pm-1:00pm

Lunch Break

1:00pm-2:00pm

Lecture: Long read sequencing (Lecture slides)

Frederikke Pedersen

2:00am-2:15pm

Break

2:15pm-4:00pm

Exercise: Long read technology (longread exercise)(longread_exercise_answers)

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Friday, January 10

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Ancient DNA and recap test

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-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

Recap Test (Test 2024)(answers)

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

1:45pm-2:00pm

Break

2:00pm-4:00pm

Time to catch up on this week's exercises

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Monday, January 13

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Metagenomics

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

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Tuesday, January 14

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Genomic Epidemiology and group project

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 2025

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Wednesday, January 15

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CancerSeq & Project work

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

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Thursday, January 16

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Project presentation

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

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Friday, January 17

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Project work

9:00am-4:00pm

Project work

1:00pm-3:00pm

Project work/Office hours

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Monday, January 20

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Project work

9:00am-4:00pm

Project work

1:00pm-3:00pm

Project work/Office hours

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Tuesday, January 21

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Project work

9:00am-4:00pm

Project work

1:00pm-3:00pm

Project work/Office hours

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Wednesday, January 22

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Project work

9:00am-4:00pm

Project work

1:00pm-3:00pm

Project work/Office hours

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Thursday, January 23

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Project Work & Produce 1 page report

10:00am-12:00pm

Q&A: Practical information about the exam

Project work/Office hours

Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

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Friday, January 24

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Exam

9:00am-4:00pm

Written Exam