Schedule

This course is given at the University of Gothenburg. The lecture slides and lab instructions will be uploaded when the material is finalized by the responsible teacher.

Monday 18th

Room: Folke Andreasson, Medicinareg. 11
12.30-14.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
14.00-15.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
15.30-17:00 Project discussion - (Adam Ameur, Olga Vinnere Pettersson)

Tuesday 19th

Room: Ingegerd Eriksson Medicinareg. 1, Academicum
09.00-09.10 Lecture: Introduction to SciLifeLab (Eva Molin)
09.10-10.00 Lecture: Introduction to Linux (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Marcela Dávila, Mats Töpel, Magnus Alm Rosenblad)
12.00-13.00 Lunch
13.00-14.00 Lecture: Introduction to UPPMAX/UPPNEX (Martin Dahlö)
14.00-16.00 Exercise: Introduction to UPPMAX/UPPNEX (Martin Dahlö, Marcela Dávila, Mats Töpel, Magnus Alm Rosenblad)
16.00-16.20 Lecture: Introduction to File Types in Bioiformatics (Martin Dahlö)
16.20-17.15 Exercise: Introduction to File Types in Bioinformatics (Martin Dahlö, Marcela Dávila, Mats Töpel, Magnus Alm Rosenblad)

Wednesday 20th

Room: Ingegerd Eriksson Medicinareg. 1, Academicum
09.00-10.00 Lecture: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Anna Johansson)
10:15-12:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Anna Johansson, Katarina Truvé, Agata Smialowska, Mats Töpel, Magnus Alm Rosenblad)
12.00-13.00 Lunch
Room: Birgit Thilander Medicinareg. 1, Academicum
13:00-17:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part II (Anna Johansson, Katarina Truvé, Agata Smialowska, Mats Töpel, Magnus Alm Rosenblad)

Thursday 21st

Room: Folke Andreasson Medicinareg. 11
09:00-11:30 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part III (Anna Johansson, Katarina Truvé, Agata Smialowska, Mats Töpel)

11:30-12.00 Lecture: The Wallenberg Advanced Bioinformatics Initiative (WABI) and the Bioinformatics Infrastructure for Life Sciences (BILS) (Anna Johansson)

12.00-13.00 Lunch
13:00-14:00 Lecture: RNA sequencing, transcriptome and expression quantification (Thomas Källman)
Room: Ingegerd Eriksson Medicinareg. 1, Academicum
14:15-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Katarina Truvé, Agata Smialowska, Mats Töpel)
18:00-20:00 Dinner at Incontro

Friday 22nd

Room: Ingegerd Eriksson Medicinareg. 1, Academicum
09:00-12.00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Katarina Truvé, Agata Smialowska, Mats Töpel)
12.00-13.00 Lunch
13:00-15.00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Thomas Källman, Katarina Truvé, Agata Smialowska, Mats Töpel)