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

Monday
Room: Trippelrummet, E10, ground floor
09.00-09.15 Registration and Welcome (Eva Molin)
09.15-10.00 Lecture: Introduction to Linux (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Jacques Dainat, Sebastian DiLorenzo, Manfred Grabherr)
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, Jacques Dainat, Sebastian DiLorenzo, Thomas Källman)

Tuesday
Room: Trippelrummet, E10, ground floor
09.00-10.00 Lecture: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Anna Johansson)
10.00-12.00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Anna Johansson, Mahesh Panchal, Lucile Soler, Martin Dahlö)
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 II (Anna Johansson, Mahesh Panchal, Lucile Soler, Martin Dahlö)

Wednesday
Room: Trippelrummet, E10, ground floor
09.00-11.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
11.00-12.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
12.00-13.00 Lunch
13:00-14.00 Lecture: ChIP sequencing and data analysis (Agata Smialowska)
14.00-17:00 Exercise: ChIP sequencing and data analysis part I (Agata Smialowska, Thomas Källman, Mahesh Panchal, Lucile Soler)

Thursday
Room: Trippelrummet, E10, ground floor
09:00-12:00 Exercise: ChIP sequencing and data analysis part II (Agata Smialowska, Thomas Källman, Jacques Dainat, Manfred Grabherr)
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, Johan Reimegård, Agata Smialowska, Jacques Dainat)

Friday
Room: Trippelrummet, E10, ground floor
09:00-09.30 Lecture: The National Bioinformatics Infrastructure Sweden (Björn Nystedt)
09:30-12.00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Olga Dethlefsen, Pall Olason, Henrik Lantz, Johan Reimegård)
12.00-13.00 Lunch
13:00-15.00 Project discussion (Olga Vinnere Pettersson, Henrik Lantz, Manfred Grabherr)