Program 2023

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REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES


Lectures will be in person in building 303A in auditorium 45. Offline discussions will take place on Discord (https://discord.gg/4yVB6vMG2n). 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 20th of January 2023.



Course Program - January 2023


Monday, January 2


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
Tech talk group formation and group work (Lecture slides) (Student Groups 2023)
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, Nicola Vogel, Louis Kraft, 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, Nicola Vogel, Louis Kraft
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)
Peter Wad Sackett, Nicola Vogel, Louis Kraft
3:30pm-4:00pm
First look at data (First look exercise)
Peter Wad Sackett, Nicola Vogel, Louis Kraft



Tueday, January 3


Data pre-processing & Alignment

9:00am-10:45am
Data basics (Lecture slides) (Data basics exercise) (Data basics exercise answers)
Gabriel Renaud, Nicola Vogel, Louis Kraft
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, Nicola Vogel, Louis Kraft



Wednesday, January 4


Alignment & Genotyping

9:00am-9:30am
Functional Human Variation
Gabriel Renaud, (Lecture slides)
9:30am-10:15am
Alignment postprocessing & variant calling (Lecture slides)
Gabriel Renaud
10:15am-10:30am
Break
10:30am-12:00pm
Exercise: Postprocessing & variant calling (Postprocess exercise) (Postprocess_exercise_answers) (SNP calling exercise) (SNP_calling_exercise_answers)
Gabriel Renaud, Josh Rubin, Louis Kraft
12:00pm-1:00pm
Lunch Break
1:00pm-1:45pm
Lecture: de novo assembly (Lecture slides)(Handout)
Gabriel Renaud
1:45pm-2:00pm
Break
2:00pm-4:00pm
Exercise: de novo assembly (denovo exercise) (denovo solution)
Gabriel Renaud, Josh Rubin, Louis Kraft



Thursday, January 5


Metagenomics

9:00am-9:45am
Metagenomics & Binning (Lecture slides)
Asker Brejnrod
9:45am-10:00am
Break
10:00am-12:00pm
Exercise: Kaiju: Taxonomic classification (Kaiju exercise) (Kaiju solution)
Asker Brejnrod,Louis Kraft
12:00pm-1:00pm
Lunch Break
1:00pm-1:45pm
Lecture: Quantitative Metagenomics (Lecture slides)
Asker Brejnrod
1:45pm-2:00pm
Break
2:00pm-4:00pm
Exercise: Quantitative Metagenomics (QuantitativeMetagenomics) (QuantitativeMetagenomicsSolution)
Asker Brejnrod, Louis Kraft



Friday, January 6


Long read tech and recap test

9:00am-9:45am
Lecture: Long read sequencing (Lecture slides)
Shilpa Garg
9:45am-10:00am
Break
10:00am-12:00am
Exercise: Long read technology (longread exercise)(longread_exercise_answers)
Shilpa Garg, Josh Rubin, Louis Kraft
12:00pm-1:00pm
Lunch Break
1:00pm-1:45pm
Recap Test (Test 2023)(answers)
Gabriel Renaud, Josh Rubin, Louis Kraft
1:45pm-2:00pm
Break
2:00pm-4:00pm
Time to work on this week's exercises
Gabriel Renaud, Josh Rubin, Louis Kraft




Monday, January 9


RNA-seq and Ancient DNA

9:00am-9:45am
Lecture: RNAseq (Lecture slides)
Kristoffer Vitting-Seerup
9:45am-10:00am
Break
10:00am-12:00pm
Exercise: RNAseq ([shorturl.at/nzBPQ Rnaseq_exercise]) (Rnaseq_exercise_answers)
Kristoffer Vitting-Seerup, Josh Rubin, Louis Kraft
12:00pm-1:00pm
Lunch Break
1:00pm-2:00pm
Ancient DNA (Lecture slides)
Martin Sikora
2:00pm-2:15pm
Break
2:15pm-4:00pm
Exercise: Ancient DNA (Ancient DNA exercise) (Ancient_DNA_exercise_answers)
Martin Sikora, Josh Rubin, Louis Kraft


Tuesday, January 10


Genomic Epidemiology and tech talk

9:00am-9:55am
Exercise: Genomic Epidemiology (Genomic epidemiology exercise) (Genomic epidemiology solution)
Gabriel Renaud
9:55am-10:10am
Break
10:10am-12:00pm
Case story: Genomic Epidemiology (Lecture)
Pimlapas Leekitecharoenphon (Shinny)
12:00pm-1:00pm
Lunch Break
1:00pm-2:00pm
Tech talk work
Gabriel Renaud, Josh Rubin, Louis Kraft
2:00pm-4:00pm
TechTalks Presentations
Gabriel Renaud, Josh Rubin, Louis Kraft



Wednesday, January 11


CancerSeq & Project work

9:00am-9:45am
Lecture: Cancer-seq (Lecture slides)
Elena Papaleo
10:00am-12:00pm
Exercise: Cancer-seq (Cancerseq_exercise) (Cancerseq_exercise_answers)
Adrian Otamendi, Josh Rubin, Louis Kraft
12:00pm-1:00pm
Lunch Break
1:00pm-1:45pm
Projects & Group formation (Lecture slides Examples from previous courses)
Gabriel Renaud, Josh Rubin, Louis Kraft
1:45pm-4:00pm
Projects & Group formation, prepare an outline for tomorrow. please write group names in the document for 2023
Gabriel Renaud, Josh Rubin, Louis Kraft




Thursday, January 12


Project presentation

9:00am-12:00pm
Project work/Prepare your project outline for this afternoon
Gabriel Renaud, Josh Rubin, Louis Kraft
12:00pm-1:00pm
Lunch Break
1:00pm-2:00pm
Project outlines (what you will do) /Project work
Gabriel Renaud, Josh Rubin, Louis Kraft
2:00pm-4:00pm
Project work
Gabriel Renaud, Josh Rubin, Louis Kraft


Friday, January 13


Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Josh Rubin, Louis Kraft


Monday, January 16


Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Josh Rubin, Louis Kraft


Tuesday, January 17


Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Josh Rubin, Louis Kraft


Wednesday, January 18


Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Josh Rubin, Louis Kraft


Thursday, January 19


Project Work & Poster Printing

Please print your poster.
Poster guide & requirements
10:00am-12:00pm
Q&A: Practical information about the exam
Project work/Office hours
Gabriel Renaud, Josh Rubin, Louis Kraft


Friday, January 20


Poster session

9:00am-4:00pm
Poster session part (exam)