TTA Bioinformatics course – Level 1

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Date/Time
Date(s) - 21/03/2018
11:00 am - 3:00 pm

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TTA (Turning the Tide of Antimicrobial resistance) network from the University of Oslo and the Oslo University Hopsital offers a Bioinformatics course which will be held on Wednesday, March 21st 2018 at the University of Oslo.

Application deadline: March 14th 2018.

 

Content

This practical course gives a basic introduction to whole genome assembly from NGS reads and provides an overview of programs being used.

Participants in the hands-on session have to bring their own laptops (limited to 14 persons, on a first- come first-serve basis). A list of required programs including instructions on how to install them will be provided in March. Participants require no previous knowledge to attend in this beginner’s course.

Please register here.

 

Program

Part I Seminar 11.00 – 12.30: ​

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).

11.00 – 11.30  Timo Lutter (TTA) – WGS & genome assembly: Quality assessment (FastQC) and trimming

11.30 – 12.00  Nermin Zecic (TTA) – WGS & genome assembly: Mapping reads to reference genome and contig assembly

12.00 – 12.30  Ola Brynildsrud (FHI) – Introduction to comparative genomics. Identifying, characterizing and visualizing the pan-genome

12:30 – 13.00  Jon Bolin (FHI) – de novo SNP calling Lunch 

 

Part II Hands-on exercises 13.00 – 15:00:

Quick explanation of associated file types

Performing quality checks with FastQC (before and after trimming)

Trimming methods

Contig-assembly and mapping to reference genome 

 

 

 

 

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