Click the heading of a topic to see the lecture slides or lab instructions. Slides are added as the course progresses.

Monday 28/11
Room: KB.J3.02 KBF31 (Linnaeus väg 6)
09.00-09.15 Registration and Welcome, presentation of SciLifeLab (Elina Staaf)
09.15-10.00 Lecture: Introduction to Linux (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Valentin Georgiev, Jeanette Tångrot, Joakim Bygdell)
12.00-13.00 Lunch
13.00-14.00 Lecture: Introduction to UPPMAX/UPPNEX (Martin Dahlö)
14.00-17.00 Exercise: Introduction to UPPMAX/UPPNEX (Martin Dahlö, Valentin Georgiev, Jeanette Tångrot, Joakim Bygdell)

Tuesday 29/11
Room: NA326
09.00-09.30 Lecture: File types in bioinformatics (Martin Dahlö)
09.30-11.00 Exercise: File types in bioinformatics (Martin Dahlö, Valentin Georgiev, Jeanette Tångrot, Joakim Bygdell)
11.00-12.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
12.00-13.00 Lunch
13:00-15:00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
15:00-17:00 Project discussions (Olga Vinnere Pettersson, Adam Ameur, TBA)

Wednesday 30/11
Room: KB.J3.02 KBF31
09.00-10.00 Lecture: National Bioinformatics Infrastructure Sweden; Introduction to NGS data analysis (Jeanette Tångrot)
10:00-11.00 Lecture: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Pall Olason)
11.00-12.00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Pall Olason, Jeanette Tångrot, Allison Churcher, Firoj Mahmud)
12.00-13.00 Lunch
13.00-17.00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Pall Olason, Jeanette Tångrot, Allison Churcher, Firoj Mahmud)

18:00- Course dinner at TBA

Thursday 01/12
Room: NA326
09:00-12.00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part II (Jeanette Tångrot, Allison Churcher, Firoj Mahmud)
12.00-13.00 Lunch
13.00-14:00 Lecture: RNA sequencing, transcriptome and expression quantification (Olga Dethlefsen)
14.00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Olga Dethlefsen, Jeanette Tångrot, Allison Churcher, Andreas Schneider)

Friday 02/12
Room: NA326
09:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Olga Dethlefsen, Jeanette Tångrot, Allison Churcher, Andreas Schneider)
12.00-13.00 Lunch
13:00-14.00 Data management (Niclas Jareborg)
14:00-15:00 Exercise: RNA sequencing, transcriptome and expression quantification part III (Olga Dethlefsen, Jeanette Tångrot, Allison Churcher, Andreas Schneider)