Instructors:
Course Assistants:
Wednesday 15th
Room: E10:1309
09.00-09.15 Introduction (Henrik Lantz)
09.15-10.00 Lecture: NGS technologies and basic concepts (Henrik Lantz)
10.00-10.15 Coffee break
10.15-11.00 Lecture: Quality control and read trimming (Mahesh Binzer-Panchal)
11.00-12.00 Exercise: Quality control and read trimming
12.00-13.00 Lunch
13.00-14.00 Exercise: Quality control and read trimming contd.
14.00-14.30 Lecture: K-mer and contamination analysis (Mahesh Binzer-Panchal)
14.30-17.00 Exercise: K-mer and contamination analysis (inc. coffee break)
Thursday 16th
Room: E10:1309
09.00-09.30 Discussion of last day’s exercises (Henrik Lantz, Mahesh Binzer-Panchal)
09.30-10.00 Lecture: Assembly basics - Genome properties (Henrik Lantz)
10.00-10.15 Coffee break
10.15-11.00 Lecture: Illumina assembly (Mahesh Binzer-Panchal)
11.00-12.00 Exercise: Illumina assembly
12.00-13.00 Lunch
13.00-13.30 Exercise: Illumina assembly contd.
13.30-14.30 Lecture: Long Read assembly (Mahesh Binzer-Panchal)
14.30-17.00 Exercise: Long Read assembly (incl. coffee break)
Friday 17th
Room: E10:1309
09.00-09.30 Discussion of last day’s exercises (Henrik Lantz, Mahesh Binzer-Panchal)
09.30-10.15 Lecture: Assembly validation (Mahesh Binzer-Panchal)
10.15-10.30 Coffee break
10.30-12.00 Exercise: Assembly validation
12.00-13.00 Lunch
13.00-15.00 Exercise: Team Assembly project
15.00-15.15 Coffee break
15.15-17.00 Exercise discussion and wrap-up (Mahesh Binzer-Panchal, Henrik Lantz)
Note: The practical exercise sessions will be made on the UPPMAX cluster. You can find the log instructions here
solutions