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

Monday
Room: Heden
09.00-09.45 Lecture: Introduction to Linux (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Dag Ahrén, Elin Videvall)
12.00-13.00 Lunch
13.00-13.45 Lecture: Introduction to UPPMAX/UPPNEX (Martin Dahlö)
13.45-17.00 Exercise: Introduction to UPPMAX/UPPNEX (Martin Dahlö, Dag Ahrén, Elin Videvall)

Tuesday
Room: Heden
09.00-09.20 Lecture: Introduction to File Types in Bioinformatics (Martin Dahlö)
09.20-10.45 Exercise: Introduction to File Types in Bioinformatics (Martin Dahlö, Dag Ahrén)
11.00-12.00 Lecture: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Anna Johansson)
12.00-13.00 Lunch
13:00-17:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Anna Johansson, Malin Larsson, Elin Videvall)

Wednesday
Room: Heden
09:00-12:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part II (Anna Johansson, Malin Larsson, Elin Videvall)
12.00-13.00 Lunch
13:00-13.30 Lecture: The National Bioinformatics Infrastructure Sweden (Malin Larsson)
13.30-15.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
15.00-16.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
16.00-17:00 Project discussion (Adam Ameur, Olga Vinnere Pettersson, Dag Ahren)

Thursday
Room: Heden
09:45-10:45 Lecture: RNA sequencing, transcriptome and expression quantification (Dag Ahren)
11:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Dag Ahren, Markus Ringnér, Elin Videvall)
12.00-13.00 Lunch
13:00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Dag Ahren, Markus Ringnér, Elin Videvall)

Friday
Room: Heden
09:00-12.00 Exercise: RNA sequencing, transcriptome and expression quantification part III (Dag Ahren, Markus Ringnér, Elin Videvall)
12.00-13.00 Lunch
13:00-15.00 Exercise: RNA sequencing, transcriptome and expression quantification part IV (Dag Ahren, Markus Ringnér, Elin Videvall)