Mick: Created page with " '''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 [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23. Lectures and exercises will take place on Discord (https://discord.gg/Qgw9M3SZA5). Please register with your full name. Will use Discord for online classes and collaboration with your project partners. Rather than emailing questions to the teac..."

2026-09-11T12:43:28Z

Created page with " '''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 [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23. Lectures and exercises will take place on Discord (https://discord.gg/Qgw9M3SZA5). Please register with your full name. Will use Discord for online classes and collaboration with your project partners. Rather than emailing questions to the teac..."

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'''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 [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23.

Lectures and exercises will take place on Discord (https://discord.gg/Qgw9M3SZA5). Please register with your full name. Will use Discord for online classes and collaboration with your project partners. Rather than emailing questions to the teaching staff, I encourage you to post your questions on discord.

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 2026 ===

<HR>
'''Monday, January 5 (Day 1)'''
<HR>
''Introduction - Next Generation Sequencing''
<DL>
<DT>9:00am-9:30am</DT>
<DD>Introduction to course
([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_1-1-Intro.pdf Lecture slides])
</DD>
<DD>Mick Westbury</DD>

<DT>9:30am-10:00am</DT>
<dd>Introduction to NGS
([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_1-2-NGS_basics.pdf Lecture slides]) </DD>
<DD>Mick Westbury</DD>

<DT>10:00am-10:45am</DT>
<DD>The NGS revolution
([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_1-3-NGS_revolution.pdf Lecture slides])</DD>
<DD>Mick Westbury</DD>

<DT>10:45am-11:00am</DT>
<DD>''Break''</DD>

<DT>11:00am-12:00pm</DT>
<DD>Exercise: Logging on to our pupil servers ([[Logging on to pupil system]])</DD>
<DD>Mick Westbury , Amanda Gammelby Qvesel, Mads Hartmann </DD>

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

<DT>1:00pm-1:30pm</DT>
<DD>Exercise: Logging on to our pupil servers ([[Logging on to pupil system]])</DD>
<DD>Mick Westbury , Amanda Gammelby Qvesel, Mads Hartmann </DD>

<DT>1:30pm-2:15pm </DT>
<DD>Introduction to UNIX </DD>
<DD>([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])</DD>
<DD>([[Unix Exercises|Unix exercises]] – possible answers [[Unix_answers|here]])
([[Basic UNIX notes]])
([[Advanced UNIX and Pipes]])</DD>
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>

<DT>2:15pm-2:30pm</DT>
<DD>''Break''</DD>

<DT>2:30pm-3:30pm </DT>
<DD>Introduction to UNIX (continued)</DD>
<DD>([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])</DD>
<DD>([[Unix Exercises|Unix exercises]] – possible answers [[Unix_answers|here]])
([[Basic UNIX notes]])
([[Advanced UNIX and Pipes]])</DD>
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>

<DT>3:30pm-4:00pm </DT>
<DD>First look at data
([[First look exercise]])
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>

</DL>

 

<HR>
'''Tuesday, January 6 (Day 2)'''
<HR>
''Data pre-processing & Alignment''

<DL>
<DT>9:00am-9:45am </DT>
<DD>Data basics ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_2-1-Data_basics.pdf Lecture slides]) ([[Data basics exercise]]) ([[Data basics exercise answers]])</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>

<DT>9:45am-10:00am</DT>
<DD>''Break''</DD>

<DT>10:00am-12:00pm </DT>
<DD>Data pre-processing ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_2-2-QC_preprocessing.pdf Lecture slides]) ([[Data Preprocess exercise]]) ([[Data Preprocess exercise answers]])</DD>
<DD> Mick Westbury </DD>

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

<DT>1:00pm-1:45pm</DT>
<DD>Alignment ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_2-3-Alignment.pdf Lecture slides]) </DD>
<DD> Mick Westbury </DD>

<DT>1:45pm-2:00pm</DT>
<DD>''Break'' </DD>

<DT>2:00pm-4:00pm</DT>
<DD>Exercise: Alignment ([[Alignment exercise]]) ([[Alignment exercise answers]])</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DL>

 

<HR>
'''Wednesday, January 7 (Day 3)'''
<HR>

''Variant calling ''
<DL>
<DT>9:00am-9:30am</DT>
<DD>Functional Variation</DD>
<DD> Mick Westbury, ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_3-1-Functional_variation.pdf Lecture slides])</DD>

<DT>9:30am-10:15am</DT>
<DD>Variant calling part 1 ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_3-2-Preprocessing-variant_calling.pdf Lecture slides])</DD>

<DD> Mick Westbury</DD>

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

<DT>10:30am-12:00pm</DT>
<DD>Exercise: Preprocessing ([[Postprocess exercise]]) ([[Postprocess_exercise_answers]])</DD>
<DD>Exercise: variant calling part 1 ([[SNP calling exercise part 1]]) ([[SNP_calling_exercise_answers part 1]])</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>

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

<DT>1:00pm-1:45pm </DT>
<DD>Lecture: variant calling part 2 ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_3-3-Variant_filtering.pdf Lecture slides])</DD>
<DD> Mick Westbury</DD>

<DT>1:45pm-2:00pm</DT>
<DD>''Break''</DD>

<DT>2:00pm-4:00pm</DT>
<DD>Exercise: variant calling part 2 ([[SNP calling exercise part 2]]) ([[SNP_calling_exercise_answers part 2]]) </DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Thursday, January 8 (Day 4)'''
<HR>
''Assembly, annotation and RNA-seq''

<DL>

<DT>9:00am-9:45pm</DT>
<DD>Lecture: de novo assembly and genomic annotations ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_4-1-Denovo.pdf Lecture slides]) </DD>
<DD> Mick Westbury</DD>

<DT>9:45pm-10:00pm</DT>
<DD>''Break''</DD>

<DT>10:00pm-12:00pm</DT>
<DD>Exercise: de novo assembly ([[denovo exercise]]) ([[denovo solution]]) </DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>

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

<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])

<DD>Kristoffer Vitting-Seerup</DD>

<DT>1:45pm-2:00pm</DT>
<DD>''Break''</DD>

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

 

<HR>
'''Friday, January 9 (Day 5)'''
<HR>
''Ancient DNA and 3D genomics''

<DT>9:00am-10:00pm</DT>
<DD>Ancient DNA ([https://teaching.healthtech.dtu.dk/material/22126/2026/dtu_adna_2026_red.pdf Lecture slides])</DD>
<DD>Martin Sikora</DD>

<DT>10:00pm-10:15pm</DT>
<DD>''Break''</DD>

<DT>10:15pm-12:00pm</DT>
<DD>Exercise: Ancient DNA ([[Ancient DNA exercise]]) ([[Ancient_DNA_exercise_answers]])</DD>
<DD>Martin Sikora, Amanda Gammelby Qvesel, Mads Hartmann</DD>

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

<DL>
<DT>1:00pm-2:00pm </DT>
<DD>Lecture: 3D Genomics with Hi-C ([https://teaching.healthtech.dtu.dk/material/22126/2026/3D_Genomics_Workshop.pdf Lecture slides])</DD>
<DD>Juan Rodríguez</DD>

<DT>2:00am-2:15pm</DT>
<DD>''Break''</DD>

<DT>2:15pm-4:00pm</DT>
<DD>Exercise: 3D Genomics with Hi-C ([[Exercise and answers]])</DD>
<DD> Juan Rodríguez, Amanda Gammelby Qvesel, Mads Hartmann</DD>
 

 

<HR>
'''Monday, January 12 (Day 6)'''
<HR>

''Microbial genomics''
<DL>
<DT>9:00am-9:45am </DT>
<DD>Lecture: Use of next-generation (genome) sequencing in clinical microbiology ([https://teaching.healthtech.dtu.dk/22126/images/7/77/Microbial_genomics_course22126_slide1-30_compressed.pdf Lecture slides 1-30])</DD>
<DD>Rasmus Lykke Marvig</DD>

<DT>9:45am-10:00am</DT>
<DD>''Break''</DD>

<DT>10:00am-11:10am</DT>
<DD>Exercise: ([[ Microbial_genomics_exercise ]]) </DD>
<DD>Rasmus Lykke Marvig, Amanda Gammelby Qvesel, Mads Hartmann</DD>

<DT>11:10pm-12:00pm</DT>
<DD>Lecture: Use of next-generation (genome) sequencing in clinical microbiology ([https://teaching.healthtech.dtu.dk/22126/images/6/6d/Microbial_genomics_course22126_slide31-75_compressed.pdf Lecture slides 31-75])</DD>
<DD>Rasmus Lykke Marvig</DD>

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

<DT>1:00pm-4:00pm</DT>
<DD>Exercise: ([[ Microbial_genomics_exercise ]]) </DD>
<DD>Rasmus Lykke Marvig, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Tuesday, January 13 (Day 7)'''
<HR>

''Phylogenomics''

<DD> The same exercise page will be used throughout the day: ([[Exercise]]) ([[Solution]])</DD>

<DL>
<DT>9:00am-9:55am</DT>
<DD>Lecture 1 + exercise: Tree thinking ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_1_Tree_thinking.pdf Lecture slides])</DD>
<DD>David Duchene, Amanda Gammelby Qvesel, Mads Hartmann</DD>

<DT>10:00am-10:55am</DT>
<DD>Lecture 2 + exercise: Data ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_2_Data.pdf Lecture slides])</DD>
<DD>David Duchene, Amanda Gammelby Qvesel, Mads Hartmann</DD>

<DT>11:00am-11:55am</DT>
<DD>Lecture 3 + exercise: Basic methods ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_3_Basic_methods.pdf Lecture slides])</DD>
<DD>David Duchene, Amanda Gammelby Qvesel, Mads Hartmann</DD>

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

<DT>1:00am-1:55am</DT>
<DD>Lecture 4 + exercise: Models and support ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_4_Models_and_support.pdf Lecture slides])</DD>
<DD>David Duchene, Amanda Gammelby Qvesel, Mads Hartmann</DD>

<DT>2:00am-2:55am</DT>
<DD>Lecture 5 + exercise: Gene trees ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_5_Gene_trees.pdf Lecture slides])</DD>
<DD>David Duchene, Amanda Gammelby Qvesel, Mads Hartmann</DD>

<DT>3:00am-3:55am</DT>
<DD>Lecture 6 + exercise: Molecular dating ([https://teaching.healthtech.dtu.dk/material/22126/2026/Lecture_6_MolecularDating.pdf Lecture slides])</DD>
<DD>David Duchene, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Wednesday, January 14 (Day 8)'''
<HR>
''Metabarcoding and group project''
<DL>
<DT>9:00am-9:55am</DT>
<DD>Metabarcoding ([https://teaching.healthtech.dtu.dk/material/22126/2026/Metabarcoding_slides.pdf Lecture slides])</DD>
<DD>Luke Holman</DD>

<DT>9:55am-10:10am</DT>
<DD>''Break''</DD>

<DT>10:10am-12:00pm</DT>
<DD>Exercise: Metabarcoding ([https://github.com/leholman/25.DTUmetabarcodingExercise/blob/main/README.md Metabarcoding Exercises]) </DD>
<DD> Luke Holman, Amanda Gammelby Qvesel, Mads Hartmann</DD>

<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/22126/2026/Recap_test.pdf Test])([https://teaching.healthtech.dtu.dk/material/22126/2026/Recap_test_Answers.pdf Answers])</DD>
<DD> Mick Westbury</DD>

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

<DT>1:45pm-2:30pm </DT>
<DD>Projects & Group formation ([https://teaching.healthtech.dtu.dk/material/22126/2026/Poster.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/1W5HzThk4zSi2xAE4dwmtgw35JtyNbwhuizseiLrxLr0/edit?usp=sharing document for 2026]</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

</DL>
 

<HR>
'''Thursday, January 15 (Day 9)'''
<HR>
''Project work''
<DL>
<DT>10:00am-12:00pm</DT>
<DD>Project consolation, check when your 3 minutes are [https://docs.google.com/spreadsheets/d/1eZeAo0jtpUcJpd7ti8h2ofjVJD8wYOUws9QMZwp0fQ8/edit?usp=sharing Timesheet]</DD>

<DD></DD>

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

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Friday, January 16 (Day 10)'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Monday, January 19 (Day 11)'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Tuesday, January 20 (Day 12)'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Wednesday, January 21 (Day 13)'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD> Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>

 

<HR>
'''Thursday, January 22 (Day 14)'''
<HR>
''Project Work & Submit poster''
<DL>

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

 

<HR>
'''Friday, January 23 (Day 15)'''
<HR>
''Exam''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Written Exam</DD>
</DL>

Program 2027 - Revision history