Summer School in Bioinformatics

Dates

 

7th-11th September  2020

Due to the COVID-19 outbreak, this course will be held online

 

 

General Topic: Understanding and Working with Next Generation Sequencing Data

 

Overview

 

 This course will introduce participants into the field of Next Generation Sequencing biology, understanding both the concepts and handling of the data. We will cover a broad range of software and analyses from quality assessment of sequencing runs, through assembling and annotating small genomes, RNAseq and differential gene expression, and phylogenomics with NGS data. Primarily focussed on Illumina data, we will also look at the different requirements and opportunities when utilising long read data (Nanopore/PacBio). This course will be accompanied with sessions on the use of the Linux command line, and docker which is the preferred platform for most bioinformatic analyses, as well as software containers, through Docker or Singularity, with particular focus on best practices for reproducibility.

 

 

Format

 

The course is structured in modules over five days. Each session will include an introductory lecture with class discussion of key concepts. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of both mirroring exercises (delivered via live coding)  with the instructors to demonstrate a skill, as well as applying these skills on your own to complete individual exercises. After and during each exercise, interpretation of results will be discussed as a group.

 

 

Target audience and assumed background

 

The course is aimed at researchers with a biological background but with no to basic hands-on experience with NGS data.  We will start by gaining experience with the Linux command line which is fundamental for running the analysis that the rest of the week will be based on. We will therefore dedicate one day to introduce basic and advanced Linux concepts for processing data on Amazon cloud (AWS), and then introduce concepts and background on each analysis step as we progress. Overall, we will begin with assessing raw sequencing data and move through genomic, transcriptomic, and phylogenetic/phylogenomic analysis.

 

 

Learning outcomes

 

Effectively handling NGS data comfortably and in a reliable and reproducible manner

Understanding the strengths and pitfalls of NGS and how to assess quality of data generation and analysis

Hands-on experience of state of the art methods to use NGS in experiments across a range of approaches (genomics, transcriptomics, phylogenomics)

Assessment of strengths and weaknesses of the different DNA sequencing technologies, both short read (Illumina), and long reads (Pacific Bioscience,Oxford Nanopore).

Familiarity with biological sequence analysis in an evolutionary context

 

 

Example data


 

 - We will use example data from Illumina and Nanopore sequencing runs across a range of species and experimental designs.

 

 - We encourage the participants to bring, analyze (if possible) and discuss their own data

 

Program

Monday - 2-8 pm Berlin time

 

Logging on to Your Personal Cloud Image
Introduction to Linux – an environment for Bioinformatics
Docker and Singularity for reproducible bioinformatics

 

InstructorS

 

 

 

Christoph Hahn, PhD

 

 

 

 

 

 

Daniel A. Pass, PhD

 

COst overview


Cancellation Policy:

 

 

 

> 30  days before the start date = 30% cancellation fee

 

< 30 days before the start date= No Refund.

 

 

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.