IBA/TTA Bioinformatics course – Level 1

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Date(s) - 26/01/2022
1:00 pm - 3:30 pm

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Wednesday, January 26th 2022

Time: 13.00-15.30

Venue: University of Oslo, DM4 Domus Medica, L-257

Registration: https://nettskjema.no/a/243002

N.B. due to the short length, IBA does not cover travel/accommodation costs for this course.

This course will give you basic knowledge on whole genome assembly, including quality assessment of raw data (FastQC), adapter / quality trimming and contig assembly. You will also learn about the differences between De novo assembly and mapping to an annotated reference genome.

Participants must bring their own laptops (limited to max 6 persons, on a first-come first-serve basis).

This course is organised by TTA in collaboration with the Research school IBA, and therefore there are spots reserved for IBA members.

We will provide Geneious educational licenses and a list of required preparations for the hands-on part one week before the course. You do not need any previous knowledge to attend this beginner’s course.

We will organize more advanced bioinformatics courses later this year for which level 1 is a requirement to sign up.

Depending on the number of applicants, we will organize a repetition of this course on February 2nd if needed. Places will be offered on a first-come first-serve basis, and if you are not among the first 8 registrations, we will offer you a place in one of the repetition courses instead.

Course schedule

Wednesday, September 8th 2021

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