Program 2026: Difference between revisions

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Lectures will be in person in building [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23.  
Lectures will be in person in building [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23.  


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Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your full name. Will use Discord for online classes and collaboration with your project partners.
Lectures and exercises will take place on Discord (https://discord.gg/mgFJxM3W). 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'''.  
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'''.  
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'''For the laptop ''' if you have a secure laptop (e.g. work laptop from Statens Serum Institut for instance), please bring your personal laptop.
'''For the laptop ''' if you have a secure laptop (e.g. work laptop from Statens Serum Institut for instance), please bring your personal laptop.
   
   
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This term, we will be using Piazza for class discussion. The system is highly catered to getting you help fast and efficiently from classmates, the TA, and myself. Rather than emailing questions to the teaching staff, I encourage you to post your questions on Piazza [https://piazza.com/class/kjernxm6wre7ck here]
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=== Course Program - January 2025 ===
=== Course Program - January 2025 ===
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<HR>
<HR>
'''Monday, January 5'''
'''Monday, January 5 (Day 1)'''
<HR>
<HR>
''Introduction - Next Generation Sequencing''
''Introduction - Next Generation Sequencing''
Line 43: Line 38:


<DT>10:00am-10:45am</DT>
<DT>10:00am-10:45am</DT>
<DD>2nd and 3rd generation NGS Technologies
<DD>The NGS revolution
([https://teaching.healthtech.dtu.dk/material/22126/2025/13_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>Mick Westbury</DD>
<DD>Mick Westbury</DD>
Line 62: Line 57:


<DT>1:30pm-2:15pm </DT>
<DT>1:30pm-2:15pm </DT>
<DD>Introduction to UNIX  
<DD>Introduction to UNIX </DD>
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])  
<DD>([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])</DD>
([[Unix Exercises|Unix exercises]] – possible answers [[Unix_answers|here]])  
<DD>([[Unix Exercises|Unix exercises]] – possible answers [[Unix_answers|here]])
([https://teaching.healthtech.dtu.dk/22126/index.php/Unix_notes Unix Notes])</DD>
([[Basic UNIX notes]])
([[Basic UNIX notes]])  
([[Advanced UNIX and Pipes]])</DD>
([[Advanced UNIX and Pipes]])  
 
 
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>


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<DT>2:30pm-3:30pm </DT>
<DT>2:30pm-3:30pm </DT>
<DD>Introduction to UNIX (continued)
<DD>Introduction to UNIX (continued)</DD>
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])  
<DD>([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])</DD>
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Exercises] possible answers [[Unix_answers|here]])
<DD>([[Unix Exercises|Unix exercises]] – possible answers [[Unix_answers|here]])
([https://teaching.healthtech.dtu.dk/22126/index.php/Unix_notes Unix Notes])</DD>
([[Basic UNIX notes]])
([https://teaching.healthtech.dtu.dk/22126/index.php/Unix_pipes Intro. to UNIX pipes])</DD>
([[Advanced UNIX and Pipes]])</DD>  
 
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>


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<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>


<DT>3:30pm-4:00pm </DT>
<DD>If you are done, some UNIX with zip codes
([[Zip codes]])
<DD>Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann </DD>
</DL>
</DL>


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<HR>
<HR>
'''Tuesday, January 6'''
'''Tuesday, January 6 (Day 2)'''
<HR>
<HR>
''Data pre-processing & Alignment''
''Data pre-processing & Alignment''
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<HR>
<HR>
'''Wednesday, January 7'''
'''Wednesday, January 7 (Day 3)'''
<HR>
<HR>


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<DL>
<DL>
<DT>9:00am-9:30am</DT>
<DT>9:00am-9:30am</DT>
<DD>Functional Human Variation</DD>
<DD>Functional Variation</DD>
<DD> Mick Westbury, ([https://teaching.healthtech.dtu.dk/material/22126/2025/41_Functional_Human_Variation_GR.pdf Lecture slides])</DD>
<DD> Mick Westbury, ([https://teaching.healthtech.dtu.dk/material/22126/2025/41_Functional_Human_Variation_GR.pdf Lecture slides])</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/22126/2025/43_post_alignment_variantcalling_part2_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])</DD>
<DD> Mick Westbury</DD>
<DD> Mick Westbury</DD>


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<HR>
<HR>
'''Thursday, January 8'''
'''Thursday, January 8 (Day 4)'''
<HR>
<HR>
''Assembly, annotation and RNA-seq''
''Assembly, annotation and RNA-seq''
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<HR>
<HR>
'''Friday, January 9'''
'''Friday, January 9 (Day 5)'''
<HR>
<HR>
''Ancient DNA and 3D genomics''
''Ancient DNA and 3D genomics''
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<HR>
<HR>
'''Monday, January 12'''
'''Monday, January 12 (Day 6)'''
<HR>
<HR>


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


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<HR>
<HR>
'''Wednesday, January 14'''
'''Wednesday, January 14 (Day 8)'''
<HR>
<HR>
''Metabarcoding and group project''
''Metabarcoding and group project''
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<HR>
<HR>
'''Thursday, January 15'''
'''Thursday, January 15 (Day 9)'''
<HR>
<HR>
''Project presentation''
''Project presentation''
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<HR>
<HR>
'''Friday, January 16'''
'''Friday, January 16 (Day 10)'''
<HR>
<HR>
''Project work''
''Project work''
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<HR>
<HR>
'''Monday, January 19'''
'''Monday, January 19 (Day 11)'''
<HR>
<HR>
''Project work''
''Project work''
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<HR>
<HR>
'''Tuesday, January 20'''
'''Tuesday, January 20 (Day 12)'''
<HR>
<HR>
''Project work''
''Project work''
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<HR>
<HR>
'''Wednesday, January 21'''
'''Wednesday, January 21 (Day 13)'''
<HR>
<HR>
''Project work''
''Project work''
Line 442: Line 429:


<HR>
<HR>
'''Thursday, January 22'''
'''Thursday, January 22 (Day 14)'''
<HR>
<HR>
''Project Work & Produce poster''
''Project Work & Produce poster''
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<HR>
<HR>
'''Friday, January 23'''
'''Friday, January 23 (Day 15)'''
<HR>
<HR>
''Exam''
''Exam''

Latest revision as of 15:01, 3 December 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.


Lectures and exercises will take place on Discord (https://discord.gg/mgFJxM3W). 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 2025

Monday, January 5 (Day 1)

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
The NGS revolution (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)
Mick Westbury , Amanda Gammelby Qvesel, Mads Hartmann
12:00pm-1:00pm
Lunch Break
1:00pm-1:30pm
Exercise: Logging on to our pupil servers (Logging on to pupil system)
Mick Westbury , Amanda Gammelby Qvesel, Mads Hartmann
1:30pm-2:15pm
Introduction to UNIX
(Video lectures to watch from "Unix intro.." to "Touching upon...")
(Unix exercises – possible answers here) (Basic UNIX notes) (Advanced UNIX and Pipes)
Mick Westbury, 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...")
(Unix exercises – possible answers here) (Basic UNIX notes) (Advanced UNIX and Pipes)
Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
3:30pm-4:00pm
First look at data (First look exercise)
Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann


Tuesday, January 6 (Day 2)

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 (Day 3)

Variant calling

9:00am-9:30am
Functional 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)
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 (Day 4)

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

Friday, January 9 (Day 5)

Ancient DNA and 3D genomics

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 ([])
Juan Rodríguez
2:00am-2:15pm
Break
2:15pm-4:00pm
Exercise: 3D Genomics with Hi-C (Hi-C exercise)(Hi-C_exercise_answers)
Juan Rodríguez, Amanda Gammelby Qvesel, Mads Hartmann


Monday, January 12 (Day 6)

Microbial genomics

9:00am-9:45am
TBA ([ Lecture slides])
Rasmus Lykke Marvig
9:45am-10:00am
Break
10:00am-12:00pm
Exercise: TBA (exercise) (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 (Questions) (Solution)
Rasmus Lykke Marvig, Amanda Gammelby Qvesel, Mads Hartmann


Tuesday, January 13 (Day 7)

Phylogenomics

9:00am-9:55am
TBA ([])
David Duchene
9:55am-10:10am
Break
10:10am-12:00pm
Exercise: TBA (Exercise) (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 (Exercises) (Solution)
David Duchene, Amanda Gammelby Qvesel, Mads Hartmann



Wednesday, January 14 (Day 8)

Metabarcoding and group project

9:00am-9:55am
TBA ([ Lecture])
Luke Holman
9:55am-10:10am
Break
10:10am-12:00pm
Exercise: TBA (Metabarcoding Exercise) (Metabarcoding 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 (Day 9)

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 (Day 10)

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 (Day 11)

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 (Day 12)

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 (Day 13)

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 (Day 14)

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 (Day 15)

Exam

9:00am-4:00pm
Written Exam
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