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OVERVIEW

We will cover a broad range of software and analysis workflows that extend over the spectrum from assembling and annotating eukaryotic genomes, via the identification of single nucleotide variants (SNVs) and structural variants (SVs) within the population, to the assessment of their likely functional impact of the detected variants in an evolutionary context.

TARGETED AUDIENCE & ASSUMED BACKGROUND

The course is aimed at researchers interested in learning how to compare genomes and what can be learned from genomic similarities as well as variations. It will include information useful for both beginners and more advanced users. We will start by introducing general concepts of comparative genomics. On this basis, we will then continue to describe all major analysis steps from the raw sequencing data via the identification of variations to an assessment of their impact on the phenotype.

Attendees should have a background in biology. There will be a mix of lectures and hands-on practical exercises using command line Linux. We will therefore dedicate one session to introduce basic and advanced Linux concepts for processing data on Amazon cloud (AWS). Attendees should have also some familiarity with genomic data such as that arising from NGS sequencing experiments.

LEARNING OUTCOMES

Setting up a comparative genomics analysis environment with the CONDA package management system
Identification of SNPs and SVs using de novo genome assembly and read mapping strategies
Assessment of strengths and weaknesses of the different DNA sequencing technologies, Illumina, Pacific Bioscience, Oxford Nanopore, for the detection of variations
Strengths and pitfalls of de novo assembly and mapping approaches for comparative genomics
Hands on experience of state of the art methods to compare multiple genomes
Annotation of variations and comparative genomics analysis
Familiarity with biological sequence analysis in an evolutionary context

INSTRUCTORS

Dr Fritz J. Sedlazeck (https://fritzsedlazeck.github.io)
Prof. Dr. Ingo Ebersberger (https://scholar.google.com/citations?user=LOOY3kYAAAAJ&hl=en)

For more information about the course, please visit our website.

Here is the full list of our courses and Workshops: https://www.physalia-courses.org/courses-workshops/

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