Schedule

This course is given at Navet (E10) at BMC. Click the heading of a topic to see the lecture slides or lab instructions.

Monday 14th

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
10.15-10.45 Lecture: Quality control and read trimming (Mahesh Panchal)
10.45-12.00 Exercise: Quality control and read trimming (solutions) (Mahesh Panchal, Henrik Lantz, Martin Norling, Lucile Soler)
12.00-13.00 Lunch
13.00-13.45 Lecture: Kmer-analysis, contamination analysis, and mapping-based analysis (Mahesh Panchal)
13.45-15.00 Exercise: Kmer-analysis, contamination analysis, and mapping-based analysis (solutions) (Mahesh Panchal, Henrik Lantz, Martin Norling, Lucile Soler)
15.00-15.15 Coffee break
15.15-16.30 Team based exercise on quality control (solutions) (Mahesh Panchal, Henrik Lantz, Martin Norling, Lucile Soler)

Tuesday 15th

Room: E10:1309
09.00-09.30 Discussion of last day’s exercises (Henrik Lantz, Mahesh Panchal, Martin Norling)
09.30-10.00 Lecture: Assembly basics - Genome properties (Henrik Lantz)
10.00-10.15 Coffee break
10.15-11.00 Lecture: Illumina assembly (Martin Norling)
11.00-12.00 Exercise: Illumina assembly (Martin Norling, Mahesh Panchal, Henrik Lantz)
12.00-13.00 Lunch
13.00-13.30 Exercise: Illumina assembly contd. (Martin Norling, Mahesh Panchal, Henrik Lantz)
13.30-14.30 Lecture: PacBio assembly, assembly polising, and demonstration of SMRT-portal (Mahesh Panchal)
14.30-17.00 Exercise: PacBio assembly (incl. coffee break) (Mahesh Panchal, Martin Norling, Henrik Lantz)

Wednesday 16th

Room: E10:1309
09.00-09.30 Discussion of last day’s exercises (Mahesh Panchal, Martin Norling)
09.30-10.00 Lecture: Assembly assessment (Martin Norling)
10.00-10.15 Coffee break
10.15-11.00 Exercise: Assembly assessment (Martin Norling, Mahesh Panchal, Henrik Lantz, Jaques Dainat)
11.00-11.30 Lecture: Assembly validation (Martin Norling)
11.30-12.00 Exercise: Assembly validation (Martin Norling, Mahesh Panchal, Henrik Lantz, Jaques Dainat)
12.00-13.00 Lunch
13.00-13.30 Lecture: Contamination assessment (Martin Norling)
13.30-15.00 Exercise: Assembly validation contd. + contamination assessment (Martin Norling, Mahesh Panchal, Henrik Lantz, Jaques Dainat)
15.00-15.15 Coffee break
15.15-15.30 Exercise discussion (Martin Norling)
15.30-17.00 Wrap-up and project discussion (Martin Norling, Mahesh Panchal, Henrik Lantz)

Note: The practical exercise sessions will be made on the UPPMAX cluster. You can find the log instructions here