Overview

 This course will introduce participants to 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 by 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 a 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 a class discussion of key concepts. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of 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, the 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 no 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 the quality of data generation and analysis

- Hands-on experience with 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 data

Monday - 2-8 pm Berlin time

Accessing the bioinformatics cloud Image
Review of Linux basics - Presentation | Practical
NGS data and Quality Control - How well did my sequencing run work? - Presentation | Practical
Linux methods for multiple sample handling - Practical

Tuesday- 2-8 pm Berlin time
Using Docker & Singularity for reproducible bioinformatics - Presentation | Practical
Short-read Genome Assembly - Presentation | Practical
Assessing Assembly Quality - Presentation | Practical

Wednesday- 2-8 pm Berlin time
Assembly with long read data - Nanopore/PacBio & hybrid assemblies - Presentation | Practical
Genome Annotation - Presentation | Practical
Genome Visualisation - Presentation | Practical

Thursday- 2-8 pm Berlin time

Phylogenetics and Phylogenomics - Presentation | Practical
Bioinformatic analysis with pipelines - Presentation | Practical

Friday- 2-8 pm Berlin time
RNAseq Processing and Transcriptomics - Presentation | Practical
Differential Gene Analysis - Presentation | Practical
Downstream RNAseq Interpretation - Presentation | Practical

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.