Program 2025: Difference between revisions

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'''NOTE: THIS PAGE IS UNDER CONSTRUCTION WITH A NEW TEACHER IN 2026'''


'''REMEMBER TO BRING A LAPTOP FOR EXERCISES'''
'''REMEMBER TO BRING A LAPTOP FOR EXERCISES'''
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<DD>''Break'' </DD>
<DD>''Break'' </DD>


 
<DT>2:30pm-4:00pm</DT>
<DT>2:30pm-2:45pm</DT>
<DD>Brief reminder on probabilities and Bayesian theory ([https://teaching.healthtech.dtu.dk/material/22126/2025/24_Bayesian_reminder_GR.pdf Lecture slides]) </DD>
<DD> Mick Westbury</DD>
 
<DT>2:45pm-4:00pm</DT>
<DD>Exercise: Alignment ([[Alignment exercise]]) ([[Alignment exercise answers]])</DD>
<DD>Exercise: Alignment ([[Alignment exercise]]) ([[Alignment exercise answers]])</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
Line 255: Line 252:
<DT>2:15pm-4:00pm</DT>
<DT>2:15pm-4:00pm</DT>
<DD>Exercise: 3D Genomics with Hi-C ([[longread exercise]])([[longread_exercise_answers]])</DD>
<DD>Exercise: 3D Genomics with Hi-C ([[longread exercise]])([[longread_exercise_answers]])</DD>
<DD> Juan Rodríguez, Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD> Juan Rodríguez, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<BR>
<BR>


Line 267: Line 264:
<HR>
<HR>


''Metagenomics''
''Microbial genomics''
<DL>
<DL>
<DT>9:00am-9:45am </DT>
<DT>9:00am-9:45am </DT>
<DD>Metagenomics & Binning ([https://teaching.healthtech.dtu.dk/material/22126/2024/Metagenomics_binning.pdf Lecture slides])</DD>
<DD>TBA ([https://teaching.healthtech.dtu.dk/material/22126/2024/Metagenomics_binning.pdf Lecture slides])</DD>
<DD>Trine Zachariasen</DD>
<DD>Rasmus Lykke Marvig</DD>


<DT>9:45am-10:00am</DT>
<DT>9:45am-10:00am</DT>
Line 277: Line 274:


<DT>10:00am-12:00pm</DT>
<DT>10:00am-12:00pm</DT>
<DD>Exercise: Kaiju: Taxonomic classification ([[Kaiju exercise]]) ([[Kaiju solution]]) </DD>
<DD>Exercise: TBA ([[Kaiju exercise]]) ([[Kaiju solution]]) </DD>
<DD>Trine Zachariasen, Cecilie Thystrup, Amanda Gammelby Qvesel</DD>
<DD>Rasmus Lykke Marvig, Amanda Gammelby Qvesel, Mads Hartmann</DD>
 
 


<DT>12:00pm-1:00pm </DT>
<DD>''Lunch Break'' </DD>


<DT>1:00pm-1:45pm</DT>
<DT>1:00pm-1:45pm</DT>
<DD>Lecture: Quantitative Metagenomics ([https://teaching.healthtech.dtu.dk/material/22126/2024/Quantitative_metagenomics.pdf Lecture slides])</DD>
<DD>Lecture: TBA ([https://teaching.healthtech.dtu.dk/material/22126/2024/Quantitative_metagenomics.pdf Lecture slides])</DD>
<DD>Trine Zachariasen</DD>
<DD>Rasmus Lykke Marvig</DD>


<DT>1:45pm-2:00pm</DT>
<DT>1:45pm-2:00pm</DT>
Line 291: Line 288:


<DT>2:00pm-4:00pm</DT>
<DT>2:00pm-4:00pm</DT>
<DD>Exercise: Quantitative Metagenomics ([[QuantitativeMetagenomics]]) ([[QuantitativeMetagenomicsSolution]]) </DD>
<DD>Exercise: TBA ([[QuantitativeMetagenomics]]) ([[QuantitativeMetagenomicsSolution]]) </DD>
<DD>Trine Zachariasen, Cecilie Thystrup, Amanda Gammelby Qvesel</DD>
<DD>Rasmus Lykke Marvig, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>
</DL>


Line 301: Line 298:
<HR>
<HR>


''Genomic Epidemiology and group project''
''Phylogenomics''


<DL>
<DL>
<DT>9:00am-9:55am</DT>
<DT>9:00am-9:55am</DT>
<DD>Case story: Genomic Epidemiology ([https://teaching.healthtech.dtu.dk/material/22126/2025/Genomic_epidemiology_NGScourse_Jan2025.pdf Lecture])</DD>
<DD>TBA ([https://teaching.healthtech.dtu.dk/material/22126/2025/Genomic_epidemiology_NGScourse_Jan2025.pdf Lecture])</DD>
<DD>Pimlapas Leekitecharoenphon (Shinny)</DD>
<DD>David Duchene</DD>


<DT>9:55am-10:10am</DT>
<DT>9:55am-10:10am</DT>
Line 312: Line 309:


<DT>10:10am-12:00pm</DT>  
<DT>10:10am-12:00pm</DT>  
<DD>Exercise: Genomic Epidemiology ([[Genomic epidemiology exercise]]) ([[Genomic epidemiology solution]])</DD>
<DD>Exercise: TBA ([[Genomic epidemiology exercise]]) ([[Genomic epidemiology solution]])</DD>
<DD> Mick Westbury</DD>
<DD> David Duchene</DD>


<DT>12:00pm-1:00pm </DT>
<DT>12:00pm-1:00pm </DT>
<DD>''Lunch Break'' </DD>
<DD>''Lunch Break'' </DD>


<DT>1:00pm-1:45pm</DT>
<DD>Lecture: TBA ([https://teaching.healthtech.dtu.dk/material/22126/2024/Quantitative_metagenomics.pdf Lecture slides])</DD>
<DD>David Duchene</DD>


<DT>1:00pm-1:45pm </DT>  
<DT>1:45pm-2:00pm</DT>
<DD>Projects & Group formation ([https://teaching.healthtech.dtu.dk/material/22126/2025/82_Projects_GR.pdf Lecture slides] [http://teaching.healthtech.dtu.dk/material/22126/2023/posters.tar.gz Examples from previous courses]) </DD>
<DD>''Break''</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>


<DT>1:45pm-4:00pm </DT>
<DT>2:00pm-4:00pm</DT>
<DD>Projects & Group formation, prepare an outline for tomorrow. please write group names in the [https://docs.google.com/document/d/11paeLyAagaIB9ytUq9ZQUaLUF8nELlt_-oxpeErFm_s/edit?usp=sharing document for 2025]</DD>
<DD>Exercise: TBA ([[QuantitativeMetagenomics]]) ([[QuantitativeMetagenomicsSolution]]) </DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD>David Duchene, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>
</DL>


</DL>


<BR>
<BR>
Line 335: Line 333:
'''Wednesday, January 14'''
'''Wednesday, January 14'''
<HR>
<HR>
''recap test & Project work''
''Metabarcoding and group project''
<DL>
<DT>9:00am-9:55am</DT>
<DD>TBA ([https://teaching.healthtech.dtu.dk/material/22126/2025/Genomic_epidemiology_NGScourse_Jan2025.pdf Lecture])</DD>
<DD>Luke Holman</DD>
 
<DT>9:55am-10:10am</DT>
<DD>''Break''</DD>


<DT>10:10am-12:00pm</DT>
<DD>Exercise: TBA ([[Genomic epidemiology exercise]]) ([[Genomic epidemiology solution]])</DD>
<DD> Luke Holman</DD>


<DT>9:00am-10am</DT>
<DT>12:00pm-1:00pm </DT>
<DD>''Lunch Break'' </DD>
 
<DT>1:00pm-1:30pm </DT>  
<DD> Recap Test ([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024.pdf Test 2025])([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024_withA.pdf answers])</DD>
<DD> Recap Test ([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024.pdf Test 2025])([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024_withA.pdf answers])</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>


<DT>10am-10:15am</DT>
<DT>1:30pm-1:45pm</DT>
<DD>''Break''</DD>
<DD>''Break''</DD>


<DT>10:15am-12pm</DT>
<DT>1:45pm-2:30pm </DT>  
<DD>Time to work on this week's exercises</DD>
<DD>Projects & Group formation ([https://teaching.healthtech.dtu.dk/material/22126/2025/82_Projects_GR.pdf Lecture slides] [http://teaching.healthtech.dtu.dk/material/22126/2023/posters.tar.gz Examples from previous courses]) </DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
 
<DT>2:30pm-4:00pm </DT> 
<DD>Projects & Group formation, prepare an outline for tomorrow. please write group names in the [https://docs.google.com/document/d/11paeLyAagaIB9ytUq9ZQUaLUF8nELlt_-oxpeErFm_s/edit?usp=sharing document for 2025]</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>
</DL>


This is the cancer-seq lecture from previous years if you would like to see it:
<DD>Lecture: Cancer-seq ([https://teaching.healthtech.dtu.dk/material/22126/2024/Cancer_Genomics_EP_2024.pdf Lecture slides]) </DD>
<DD>Elena Papaleo </DD>
<DD>Exercise: Cancer-seq ([[Cancerseq_exercise]]) ([[Cancerseq_exercise_answers]])</DD>
</DL>
</DL>
<DT>12:00pm-1:00pm </DT>
<DD>''Lunch Break'' </DD>
<DT>1:00pm-4:00pm </DT>
<DD>Project consulation</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<BR>
<BR>


Revision as of 13:21, 17 November 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

Wednesday, January 7

Variant calling

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


Thursday, January 8

Assembly, annotation and RNA-seq

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
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, Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann


Friday, January 9

Ancient DNA and RNAseq

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


Monday, January 12

Microbial genomics

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


Tuesday, January 13

Phylogenomics

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



Wednesday, January 14

Metabarcoding and group project

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


Thursday, January 15

Project presentation

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


Friday, January 16

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann


Monday, January 19

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann


Tuesday, January 20

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann


Wednesday, January 21

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann


Thursday, January 22

Project Work & Produce poster

10:00am-12:00pm
Q&A: Practical information about the exam
Project work/Office hours
Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann


Friday, January 23

Exam

9:00am-4:00pm
Written Exam
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