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Overview

Bioinformatics is a must-have skill required in every modern research lab. This course will explore the fundamentals of bioinformatics analysis. The participants will be provided with end-to-end hands-on training, along with an introduction to basic concepts, in using popular tools. Participants will gain an understanding of bioinformatics analysis in the context of aquaculture research. The key learning objectives are for participants to understand the utility of NGS for a range of aquaculture-related objectives and bioinformatics pipelines for NGS data, and to gain knowledge of specific pipelines for RADseq and RNAseq protocols.

Course content

Training will be provided through blended learning elements such as lectures, practical exercises and a mini industry seminar.

Lectures topics will include

  • Unix/Linux command system and basic scripting
  • Sequence alignment (genomic and transcriptomic)
  • Variation calling (SNP)
  • RNA-Seq expression measurement
  • 16S metagenomics
  • Genome assembly with short and long reads
  • Marker development (GBS/RAD-Seq)

Target Audience

The target audience is primarily students and lab researchers who want to be introduced to bioinformatics concepts and analysis. This course is not an advanced course for bioinformatists, but rather a starter course for researchers that want to have a better understanding of their data, gain more insights or to plan experiments better and maximise the analytics output. Required competence level: basic knowledge of molecular biological methods.

Course Tutors

Dr Michaël Bekaert - University of Stirling, UK

Dr Michaël Bekaert, senior lecturer in bioinformatics and genomics, is working extensively on the genomics of fish (cyprinids, salmonids, cichlids), mussels, sea lice, pathogenic bacteria and viruses, and SNP-based genetic mapping in aquaculture. Dr Bekaert has been involved in cloud-based software solutions for next generation diagnostics in infectious diseases. More recently, Dr Bekaert has addressed questions of genetic diversity, genome assembly, and marker discovery in farmed fish.

Christophe Klopp - INRA, France

Christophe Klopp currently works at the Department of Applied Mathematics and Informatics, French National Institute for Agricultural Research. Christophe leads a group of bioinformaticians providing services to INRA, biologists working in animal genomics and co-leads the local bio-informatic Genotoul platform. These teams develop software packages, train biologists and take part in research projects.

License & Distribution

Turorials and samples can be found at https://github.com/pseudogene/aquaexcel

Except where otherwise noted, materials and tutorials on this course is licensed under a Creative Commons Attribution-ShareAlike 4.0 International license.