Program 2026: Difference between revisions
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'''Monday, January 5''' | '''Monday, January 5 (Day 1)''' | ||
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''Introduction - Next Generation Sequencing'' | ''Introduction - Next Generation Sequencing'' | ||
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'''Tuesday, January 6''' | '''Tuesday, January 6 (Day 2)''' | ||
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''Data pre-processing & Alignment'' | ''Data pre-processing & Alignment'' | ||
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'''Wednesday, January 7''' | '''Wednesday, January 7 (Day 3)''' | ||
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'''Thursday, January 8''' | '''Thursday, January 8 (Day 4)''' | ||
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''Assembly, annotation and RNA-seq'' | ''Assembly, annotation and RNA-seq'' | ||
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'''Friday, January 9''' | '''Friday, January 9 (Day 5)''' | ||
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''Ancient DNA and 3D genomics'' | ''Ancient DNA and 3D genomics'' | ||
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'''Monday, January 12''' | '''Monday, January 12 (Day 6)''' | ||
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'''Tuesday, January 13''' | '''Tuesday, January 13 (Day 7)''' | ||
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'''Wednesday, January 14''' | '''Wednesday, January 14 (Day 8)''' | ||
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''Metabarcoding and group project'' | ''Metabarcoding and group project'' | ||
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'''Thursday, January 15''' | '''Thursday, January 15 (Day 9)''' | ||
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''Project presentation'' | ''Project presentation'' | ||
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'''Friday, January 16''' | '''Friday, January 16 (Day 10)''' | ||
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''Project work'' | ''Project work'' | ||
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'''Monday, January 19''' | '''Monday, January 19 (Day 11)''' | ||
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''Project work'' | ''Project work'' | ||
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'''Tuesday, January 20''' | '''Tuesday, January 20 (Day 12)''' | ||
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''Project work'' | ''Project work'' | ||
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'''Wednesday, January 21''' | '''Wednesday, January 21 (Day 13)''' | ||
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''Project work'' | ''Project work'' | ||
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'''Thursday, January 22''' | '''Thursday, January 22 (Day 14)''' | ||
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''Project Work & Produce poster'' | ''Project Work & Produce poster'' | ||
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'''Friday, January 23''' | '''Friday, January 23 (Day 15)''' | ||
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''Exam'' | ''Exam'' | ||
Revision as of 10:40, 2 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.
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
- NGS Technologies and the future of NGS (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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 10:00am-12:00pm
- Q&A: Practical information about the exam
- Project work/Office hours
- Mick Westbury, Amanda Gammelby Qvesel, Mads Hartmann
- 9:00am-4:00pm
- Written Exam
Wednesday, January 7 (Day 3)
Variant calling
Thursday, January 8 (Day 4)
Assembly, annotation and RNA-seq
Friday, January 9 (Day 5)
Ancient DNA and 3D genomics
Monday, January 12 (Day 6)
Microbial genomics
Tuesday, January 13 (Day 7)
Phylogenomics
Wednesday, January 14 (Day 8)
Metabarcoding and group project
Thursday, January 15 (Day 9)
Project presentation
Friday, January 16 (Day 10)
Project work
Monday, January 19 (Day 11)
Project work
Tuesday, January 20 (Day 12)
Project work
Wednesday, January 21 (Day 13)
Project work
Thursday, January 22 (Day 14)
Project Work & Produce poster
Friday, January 23 (Day 15)
Exam