Date(s) - 15/12/2021
1:00 pm - 3:30 pm
Categories No Categories
IBA/TTA Bioinformatics course – Level 1.
IBA originally planned for a level 3 course on this date. This was changed due to a large interest in level 1 courses.
This course is postponed due to the recent development in corona restrictions.
Wednesday, December 15th 2021
Venue: University of Oslo, DM4 Domus Medica, L-257
Application deadline: December 8th 2021
Please register at the following link: https://nettskjema.no/a/235803
(Please note, due to the short length of the course, IBA cannot offer members support for travel/accommodation)
13.00 – 13.30 Part I: Introduction to Whole Genome Sequencing
Theoretical introduction and applications in microbial whole genome sequence analysis:
- Basic whole genome sequence assembly and bioinformatics
- NGS read-to-reference alignment (contig assembly)
Analysis techniques covered will employ raw data from Illumina platforms (HiSeq/MiSeq).
After giving a short overview of Next Generation Sequencing, paired-end reads and the difficulties of whole genome assembly, we will address quality control of the raw data (FastQC), common file types and adapter/quality trimming. Differences between De novo assembly and mapping to an annotated reference genome will be explained, and we will present different software solutions and tools.
13:30 – 13:45 Coffee break
13.45 – 15.30 Part II: Hands-on exercises
- Quick explanation of associated file types
- Performing quality checks with FastQC (before and after trimming)
- Adapter and quality trimming
- Contig assembly and mapping to reference genome
Participants must bring their own laptops (limited to 6 persons, on a first-come first-serve basis).
A list of required programs including instructions on how to install them will be provided before the course. You do not need any previous knowledge to attend this beginner’s course.
We will organize a level 2 course on January 19th 2022 for which level 1 is a requirement.
Timo Lutter & Mari Støen, TTA.