Program 2023

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
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)

Program 2023

Course Program - January 2023

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