Introduction to analysis of next (NGS) and third generation sequencing data
Overall Aim
Basic knowledge in Genetics and and Computional Biology is needed to run genetic analyses and interpret results. The goal of this course is to give students insights in both areas and present them a blueprint for large-scale studies.
Location & Time
- May 02 - May 06 2022
- Start: May 02 9:00am
- Location: Computerraum C1 (FP301200) Fritz Pregl Strasse 3, 1. OG
- Official course information
Lecturer
Stefan Coassin, Sebastian Schoenherr
Institute of Genetic Epidemiology
Medical University of Innsbruck
Timetable
Day 1 [09:00 - 16:00]
Stefan, Sebastian:
- General / Sequencing Introduction [09.00-09.30]
Stefan:
- NGS Technology Basics; Illumina; Iontorrent [9.30-11.30 including break]
- Library types Single, Paired, mate [9.30-11.30 including break]
Sebastian:
- Bioinformatics Introduction [11.30 - 12.30]
*Lunch 12.30 - 13.15
Sebastian:
- Linux Introduction [13.15 - 15.15 including 15 min break]
- Install Tools and Trim
- Exercises Day 1 [15.15-16.00]
Day 2 09:00 - 16:00
Stefan:
- Data formats: FASTQ (09.00 - 12.25)
- Look at datasets & navigate through folders (09.00 - 12.25)
- Data QC: FASTQC, multiQC (09.00 - 12.25)
- Data QC: FASTQC, multiQC Exercises (09.00 - 12.25)
*Lunch (12.25 - 13.05)
Sebastian:
- Install Tools and Trim (13.05 - 14.55)
- Bash Scripting (13.10 - 14.55)
- Introduction to Nextflow (15.10-15.45)
- Exercises Day 2 (skipped)
Day 3 09:00 - 16:20
Sebastian:
- Alignment (09.00 - 09.45)
- Alignment Exercises (09.45 - 11.10 including 15 min break)
- Tablet Viewer, Variant Calling + Simple Exercise (11.10 - 11.50)
- Exercises
*Lunch (11.50 - 13.10)
Stefan:
- Annotation, BCFTools and VCFtools (13.10 - 16.20)
Day 4 08:30 - 16:45
Stefan, Sebastian:
- Genepi Hackathon
Credits
https://github.com/quinlan-lab/applied-computational-genomics