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

Monday
Room: Campus Valla, House B, Room Odén
09.00-09.15 Registration and Welcome, presentation of SciLifeLab (Malin Larsson)
09.15-10.00 Lecture: Introduction to Linux (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Malin Larsson)
12.00-13.00 Lunch at Universitetsklubben
13.00-14.00 Lecture: Introduction to UPPMAX/UPPNEX (Martin Dahlö)
14.00-17.00 Exercise: Introduction to UPPMAX/UPPNEX (Martin Dahlö, Malin Larsson)

Tuesday
Room: Campus Valla, House B, Room Odén
09.00-10.00 Lecture: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Malin Larsson)
10.00-12.00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Malin Larsson, Mihaela Martis)
12.00-13.00 Lunch at Universitetsklubben
13:00-17:00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part II (Malin Larsson, Mihaela Martis)

Wednesday
Room: Campus Valla, House B, Room Odén
09.00-11.30 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
11:30-12.00 Lecture: The National Bioinformatics Infrastructure Sweden (Malin Larsson)
12.00-13.00 Lunch at Universitetsklubben
13.00-14.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
14.00-17.00 Project discussion (Olga Vinnere Pettersson, Adam Ameur, Malin Larsson, Mihaela Martis, Agata Smialowska)

18:00- Course dinner at De Klomp

Thursday
Room: Campus Valla, House B, Room Odén
09:00-10.00 Lecture: ChIP sequencing and data analysis (Agata Smialowska)
10.00-12:00 Exercise: ChIP sequencing and data analysis part I (Agata Smialowska, Mihaela Martis)
12.00-13.00 Lunch at Universitetsklubben
13.00-17:00 Exercise: ChIP sequencing and data analysis part II (Agata Smialowska, Mihaela Martis)

Friday
Room: Campus Valla, House B, Room Odén
09:00-10:00 Lecture: RNA sequencing, transcriptome and expression quantification (Olga Dethlefsen)
10:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part I(Olga Dethlefsen, Agata Smialowska, Mihaela Martis)
12.00-13.00 Lunch at Universitetsklubben
13:00-17.00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Olga Dethlefsen, Agata Smialowska, Mihaela Martis)