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<DT>9:00am-9:30am</DT>   
<DT>9:00am-9:30am</DT>   
<DD>Introduction to course  
<DD>Introduction to course  
([https://teaching.healthtech.dtu.dk/material/22126/2024/11_Introduction_to_course_GR.pdf Lecture slides])
([https://teaching.healthtech.dtu.dk/material/22126/2025/11_Introduction_to_course_GR.pdf Lecture slides])
</DD>
</DD>
<DD>Gabriel Renaud</DD>
<DD>Gabriel Renaud</DD>
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<DT>9:30am-10:00am</DT>
<DT>9:30am-10:00am</DT>
<dd>Introduction to NGS  
<dd>Introduction to NGS  
([https://teaching.healthtech.dtu.dk/material/22126/2024/12_Introduction_to_NGS_GR.pdf Lecture slides]) </DD>
([https://teaching.healthtech.dtu.dk/material/22126/2025/12_Introduction_to_NGS_GR.pdf Lecture slides]) </DD>
<DD>Gabriel Renaud</DD>
<DD>Gabriel Renaud</DD>


<DT>10:00am-10:45am</DT>
<DT>10:00am-10:45am</DT>
<DD>2nd and 3rd generation NGS Technologies  
<DD>2nd and 3rd generation NGS Technologies  
([https://teaching.healthtech.dtu.dk/material/22126/2024/13_Introduction_to_NGS_technology_GR.pdf Lecture slides])</DD>
([https://teaching.healthtech.dtu.dk/material/22126/2025/13_Introduction_to_NGS_technology_GR.pdf Lecture slides])</DD>
<DD>Gabriel Renaud</DD>
<DD>Gabriel Renaud</DD>


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<DL>
<DL>
<DT>9:00am-10:45am </DT>
<DT>9:00am-10:45am </DT>
<DD>Data basics ([https://teaching.healthtech.dtu.dk/material/22126/2024/21_Data_Basics_GR.pdf Lecture slides]) ([[Data basics exercise]]) ([[Data basics exercise answers]])</DD>
<DD>Data basics ([https://teaching.healthtech.dtu.dk/material/22126/2025/21_Data_Basics_GR.pdf Lecture slides]) ([[Data basics exercise]]) ([[Data basics exercise answers]])</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann </DD>


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<DT>11:00am-12:00pm </DT>
<DT>11:00am-12:00pm </DT>
<DD>Data pre-processing ([https://teaching.healthtech.dtu.dk/material/22126/2024/22_Data_Preprocessing_GR.pdf Lecture slides]) ([[Data Preprocess exercise]]) ([[Data Preprocess exercise answers]])</DD>
<DD>Data pre-processing ([https://teaching.healthtech.dtu.dk/material/22126/2025/22_Data_Preprocessing_GR.pdf Lecture slides]) ([[Data Preprocess exercise]]) ([[Data Preprocess exercise answers]])</DD>
<DD>Gabriel Renaud </DD>
<DD>Gabriel Renaud </DD>


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<DT>1:00pm-2:15pm</DT>
<DT>1:00pm-2:15pm</DT>
<DD>Alignment ([https://teaching.healthtech.dtu.dk/material/22126/2024/23_Alignment_GR.pdf Lecture slides]) </DD>
<DD>Alignment ([https://teaching.healthtech.dtu.dk/material/22126/2025/23_Alignment_GR.pdf Lecture slides]) </DD>
<DD>Gabriel Renaud </DD>
<DD>Gabriel Renaud </DD>


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<DT>2:30pm-2:45pm</DT>
<DT>2:30pm-2:45pm</DT>
<DD>Brief reminder on probabilities and Bayesian theory ([https://teaching.healthtech.dtu.dk/material/22126/2024/24_Bayesian_reminder_GR.pdf Lecture slides]) </DD>
<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>Gabriel Renaud</DD>
<DD>Gabriel Renaud</DD>


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<DT>9:00am-9:30am</DT>
<DT>9:00am-9:30am</DT>
<DD>Functional Human Variation</DD>
<DD>Functional Human Variation</DD>
<DD>Gabriel Renaud, ([https://teaching.healthtech.dtu.dk/material/22126/2024/41_Functional_Human_Variation_GR.pdf Lecture slides])</DD>
<DD>Gabriel Renaud, ([https://teaching.healthtech.dtu.dk/material/22126/2025/41_Functional_Human_Variation_GR.pdf Lecture slides])</DD>


<DT>9:30am-10:15am</DT>
<DT>9:30am-10:15am</DT>
<DD>Variant calling part 1 ([https://teaching.healthtech.dtu.dk/material/22126/2024/42_post_alignment_variantcalling_GR.pdf Lecture slides])</DD>
<DD>Variant calling part 1 ([https://teaching.healthtech.dtu.dk/material/22126/2025/42_post_alignment_variantcalling_part1_GR.pdf Lecture slides])</DD>


<DD>Gabriel Renaud</DD>
<DD>Gabriel Renaud</DD>
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<DT>1:00pm-1:45pm </DT>
<DT>1:00pm-1:45pm </DT>
<DD>Lecture: variant calling part 2 ([https://teaching.healthtech.dtu.dk/material/22126/2024/43_de_novo_assembly_course_GR.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </DD>
<DD>Lecture: variant calling part 2 ([https://teaching.healthtech.dtu.dk/material/22126/2025/43_post_alignment_variantcalling_part2_GR.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </DD>
<DD>Gabriel Renaud</DD>
<DD>Gabriel Renaud</DD>


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<DT>9:00am-10:00pm</DT>
<DT>9:00am-10:00pm</DT>
<DD>Lecture: de novo assembly and genomic annotations ([https://teaching.healthtech.dtu.dk/material/22126/2024/43_de_novo_assembly_course_GR.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </DD>
<DD>Lecture: de novo assembly and genomic annotations ([https://teaching.healthtech.dtu.dk/material/22126/2025/51_de_novo_assembly_course_GR.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </DD>
<DD>Gabriel Renaud</DD>
<DD>Gabriel Renaud</DD>


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<DL>
<DL>
<DT>1:00pm-2:00pm </DT>
<DT>1:00pm-2:00pm </DT>
<DD>Lecture: Long read sequencing ([https://teaching.healthtech.dtu.dk/material/22126/2024/Long_read_sequencing_Lecture_08-01-2023.pdf Lecture slides])</DD>
<DD>Lecture: Long read sequencing ([https://teaching.healthtech.dtu.dk/material/22126/2025/Long_read_sequencing_Lecture_09-01-2025.pptx Lecture slides])</DD>
<DD>Frederikke Pedersen</DD>
<DD>Frederikke Pedersen</DD>


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<DT>9:00am-10:00pm</DT>
<DT>9:00am-10:00pm</DT>
<DD>Ancient DNA ([https://teaching.healthtech.dtu.dk/material/22126/2024/dtu_adna_2024.pdf Lecture slides])</DD>
<DD>Ancient DNA ([https://teaching.healthtech.dtu.dk/material/22126/2025/dtu_adna_2025_red.pdf Lecture slides])</DD>
<DD>Martin Sikora</DD>
<DD>Martin Sikora</DD>


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<DT>1:00pm-1:45pm</DT>
<DT>1:00pm-1:45pm</DT>
<DD>Lecture: RNAseq ([https://teaching.healthtech.dtu.dk/material/22126/2024/ngs_transcriptomics_kvs_2023_without_solutions_v2.pdf Lecture slides]) ([https://teaching.healthtech.dtu.dk/material/22126/2024/ngs_transcriptomics_kvs_2023_with_solutions_v2.pdf Lecture slides with solutions])</DD>
<DD>Lecture: RNAseq ([https://teaching.healthtech.dtu.dk/material/22126/2024/ngs_transcriptomics_kvs_2023_without_solutions_v2.pdf Lecture slides])  
<!--
 
([https://teaching.healthtech.dtu.dk/material/22126/2024/ngs_transcriptomics_kvs_2023_with_solutions_v2.pdf Lecture slides with solutions])</DD>
-->
<DD>Kristoffer Vitting-Seerup</DD>
<DD>Kristoffer Vitting-Seerup</DD>


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<DT>2:00pm-4:00pm</DT>
<DT>2:00pm-4:00pm</DT>
<DD>Exercise: RNAseq ([[Rnaseq_exercise]]) ([[Rnaseq_exercise_answers]]) </DD>
<DD>Exercise: RNAseq ([[Rnaseq_exercise]]) <!-- ([[Rnaseq_exercise_answers]]) --> </DD>
<DD>Kristoffer Vitting-Seerup, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Kristoffer Vitting-Seerup, Amanda Gammelby Qvesel, Mads Hartmann </DD>


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<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/22126/2024/Genomic_epidemiology_NGScourse_Jan2024.pdf Lecture])</DD>
<DD>Case story: Genomic Epidemiology ([https://teaching.healthtech.dtu.dk/material/22126/2025/Genomic_epidemiology_NGScourse_Jan2025.pdf Lecture])</DD>
<DD>Pimlapas Leekitecharoenphon (Shinny)</DD>
<DD>Pimlapas Leekitecharoenphon (Shinny)</DD>


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<DT>1:00pm-1:45pm </DT>  
<DT>1:00pm-1:45pm </DT>  
<DD>Projects & Group formation ([https://teaching.healthtech.dtu.dk/material/22126/2024/82_Projects_GR.pdf Lecture slides] [http://teaching.healthtech.dtu.dk/material/22126/2024/posters.tar.gz Examples from previous courses]) </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>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>


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'''Wednesday, January 15'''
'''Wednesday, January 15'''
<HR>
<HR>
''CancerSeq & Project work''
''recap test & Project work''


<DT>9:00am-9:45am  </DT>
 
<DT>9:00am-10am</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>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann </DD>
 
<DT>10am-10:15am</DT>
<DD>''Break''</DD>
 
<DT>10:15am-12pm</DT>
<DD>Time to work on this week's exercises</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</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>Lecture: Cancer-seq ([https://teaching.healthtech.dtu.dk/material/22126/2024/Cancer_Genomics_EP_2024.pdf Lecture slides]) </DD>  
<DD>Elena Papaleo </DD>
<DD>Elena Papaleo </DD>


<DT>10:00am-12:00pm</DT>
<DD>Exercise: Cancer-seq ([[Cancerseq_exercise]]) ([[Cancerseq_exercise_answers]])</DD>
<DD>Exercise: Cancer-seq ([[Cancerseq_exercise]]) ([[Cancerseq_exercise_answers]])</DD>
<DD>Matteo Arnaudi, Amanda Gammelby Qvesel, Mads Hartmann </DD>
</DL>
</DL>


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'''Thursday, January 23'''
'''Thursday, January 23'''
<HR>
<HR>
''Project Work & Produce 1 page report''
''Project Work & Produce poster''
<DL>
<DL>


Latest revision as of 10:05, 23 January 2025

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 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

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)
(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 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

Wednesday, January 8

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 part 1) (SNP_calling_exercise_answers part 1)
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 (SNP calling exercise part 2) (SNP_calling_exercise_answers part 2)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Thursday, January 9

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


Friday, January 10

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-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

Monday, January 13

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


Tuesday, January 14

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


Wednesday, January 15

recap test & Project work


9:00am-10am
Recap Test (Test 2025)(answers)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
10am-10:15am
Break
10:15am-12pm
Time to work on this week's exercises
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


This is the cancer-seq lecture from previous years if you would like to see it:

Lecture: Cancer-seq (Lecture slides)
Elena Papaleo
Exercise: Cancer-seq (Cancerseq_exercise) (Cancerseq_exercise_answers)
12:00pm-1:00pm
Lunch Break
1:00pm-4:00pm
Project consulation
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

Thursday, January 16

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


Friday, January 17

Project work

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


Monday, January 20

Project work

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


Tuesday, January 21

Project work

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


Wednesday, January 22

Project work

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


Thursday, January 23

Project Work & Produce poster

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


Friday, January 24

Exam

9:00am-4:00pm
Written Exam
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