Schedule

This course is given at Navet (E10) at BMC. Click the heading of a topic to see the lecture slides or lab instructions.

Monday 9th
Room:
09.00-09.15 Registration and Welcome (Eva Molin)
09.15-10.30 Lecture: Introduction to Linux (Martin Dahlö)
11.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Jacques Dainat, Alvaro Martinez Barrio, Manfred Grabherr)
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, Sebastian DiLorenzo, Alvaro Martinez Barrio, Martin Norling)

Tuesday 10th
Room:
09.00-09.20 Lecture: Introduction to File Types in Bioinformatics (Martin Dahlö)
09.20-10.15 Exercise: Introduction to File Types in Bioinformatics (Martin Dahlö, Sebastian DiLorenzo, Martin Norling, Alvaro Martinez Barrio)
10.30-12.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
12.00-13.00 Lunch
13.00-14.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
14.30-17:00 Project discussion - (Adam Ameur, Olga Vinnere Pettersson, Henrik Lantz, Thomas Källman)

Wednesday 11th
Room:
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, Sebastian DiLorenzo, Jacques Dainat, Åsa Björklund)
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 II (Anna Johansson, Martin Dahlö, Jacques Dainat, Åsa Björklund)

Thursday 12th
Room:
09:00-12:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part III (Anna Johansson, Martin Dahlö, Johan Reimegård, Manfred Grabherr)
12.00-13.00 Lunch
13:00-14:00 Lecture: RNA sequencing, transcriptome and expression quantification (Thomas Källman)
14:15-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Jacques Dainat, Johan Reimegård, Martin Norling)

Friday 13th
Room:
09:00-11.00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Thomas Källman, Manfred Grabherr, Martin Norling, Pall Olason, Henrik Lantz)
11:30-12.00 Lecture: The Wallenberg Advanced Bioinformatics Initiative (WABI) and the Bioinformatics Infrastructure for Life Sciences (BILS) (Björn Nystedt)
12.00-13.00 Lunch
13:00-15.00 Exercise: RNA sequencing, transcriptome and expression quantification part III (Thomas Källman, Martin Norling, Henrik Lantz, Pall Olason)