Module: Bioinformatics Buffet

This module will cover the introductory materials of a broad range of topics in bioinformatics.

Monday: Introduction to Galaxy and Genomics

Lecture & Demo Video

Description:

This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it.
Length: 10 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

In this tutorial, we will walk you through your first (toy) analysis in Galaxy. This tutorial is aimed at familiarizing you with the Galaxy platform, and some basic NGS concepts.
Length: 1 hour 30 minutes
Captions: Natalie Kucher
Created: 18 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

In this sesssion, we will walk you through the basics of quality checking your sequencing data. This session consists of a lecture followed by a hands-on tutorial.

Quality Control (Lecture)

Description:

This lecture goes over the concepts involved in assessing the quality of your sequencing data.
Length: 40 minutes
Captions: Yvonne Hiltemann, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
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Speaker

Quality Control (Tutorial)

Description:

In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data.
Length: 50 minutes
Captions: Andrew Lonsdale
Created: 19 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
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Speaker

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Tuesday: Genomics

In this sesssion, we will walk you through the basics of mapping your sequencing data to a reference genome. This session consists of a lecture followed by a hands-on tutorial.

Mapping (Lecture)

Description:

This lecture covers the basic concepts involved in mapping sequencing reads to a reference genome.
Length: 10 minutes
Captions: Daniel Blankenberg
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

Mapping (Tutorial)

Description:

In this tutorial you will map sequencing data to a reference genome, and explore the mapped reads in a genome browser.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

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This session provides an introduction to Genome Assembly

An Introduction to Genome Assembly (Lecture)

Description:

This lecture walks you through the basic concepts involved in assembling a genome from short-read sequencing data.
Length: 25 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • assemble some paired end reads using Velvet
  • examine the output of the assembly.
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Speaker

Chloroplast genome assembly (Lecture & Tutorial)

Description:

In this tutorial, you will assemble a chloroplast genome using a combination of short and long read data.
Length: 35 minutes
Captions: Anna Syme
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Assemble a chloroplast genome from long reads
  • Polish the assembly with short reads
  • Annotate the assembly and view
  • Map reads to the assembly and view
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Speaker

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Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny.

M. tuberculosis Variant Analysis (Lecture)

Description:

Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

M. tuberculosis Variant Analysis (Tutorial)

Description:

Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny.
Length: 40 minutes
Captions: Peter van Heusden, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • How should we filter those variants
  • How can we predict drug resistance from those variants
  • How do we annotate those variants
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Speaker

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ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. This session will introduce ATAC-Seq and walk you through an analysis step by step.

ATAC-Seq data analysis (Lecture)

Description:

This lecture will introduce the basic concepts involved in ATAC-Seq analysis.
Length: 15 minutes
Captions: Lucille Delisle
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Apply appropriate analysis and quality control steps for ATAC-Seq
  • Generate a heatmap of transcription start site accessibility
  • Visualise peaks for specific regions
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Speaker

ATAC-Seq data analysis (Tutorial)

Description:

This tutorial will walk you through a ATAC-Seq data analysis.
Length: 1 hour 50 minutes
Captions: Hans-Rudolf Hotz
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Apply appropriate analysis and quality control steps for ATAC-Seq
  • Generate a heatmap of transcription start site accessibility
  • Visualise peaks for specific regions
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Speaker

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This lecture will introduce the basic concepts involved in CRISPR screen analysis.

CRISPR screen analysis (Lecture)

Description:

This lecture will introduce the basic concepts involved in CRISPR screen analysis.
Length: 3 minutes
Captions: Maria Doyle
Created: 10 March 2022
Materials:
Support:
Learning Objectives:
  • Apply appropriate analysis and quality control steps for CRISPR screen data
  • Identify differentially enriched genes across conditions
  • Generate volcano plot to visualise results
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Speaker

CRISPR screen analysis (Tutorial)

Description:

This tutorial will walk you through a CRISPR screen analysis.
Length: 45 minutes
Captions: Maria Doyle
Created: 10 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Apply appropriate analysis and quality control steps for CRISPR screen data
  • Identify differentially enriched genes across conditions
  • Generate volcano plot to visualise results
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Speaker

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Wednesday: Transcriptomics

Lecture Video

Description:

RNA sequencing is used to assess the expression levels of genes. This video introduces the important concepts related to RNA-seq analysis.
Length: 30 minutes
Captions: Nadia Goué, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
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Speaker

Tutorial Video

Description:

In this tutorial we will walk you through the process of an RNA-seq analysis, comparing gene expression levels between different conditions and assessing impacted gene pathways.
Length: 2 hours 50 minutes
CYOA: This is a Choose-Your-Own-Adventure (CYOA) tutorial! This means you will be presented with a choice at the end of the video; pick one of the paths and a new video will play. Happy Adventuring!
Captions: Lucille Delisle
Created: 15 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Check a sequence quality report generated by FastQC for RNA-Seq data
  • Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome
  • Select and run a state of the art mapping tool for RNA-Seq data
  • Evaluate the quality of mapping results
  • Describe the process to estimate the library strandness
  • Estimate the number of reads per genes
  • Explain the count normalization to perform before sample comparison
  • Construct and run a differential gene expression analysis
  • Analyze the DESeq2 output to identify, annotate and visualize differentially expressed genes
  • Perform a gene ontology enrichment analysis
  • Perform and visualize an enrichment analysis for KEGG pathways
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Speaker

Tutorial Video

Description:

This tutorial will show you how you can create volcano plots from your RNA-Seq analysis results using Galaxy tools.
Length: 10 minutes
Captions: Maria Doyle
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Create a volcano plot of RNA-seq data to visualize significant genes
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Speaker

Thursday: Proteomics

Lecture Video

Description:

This lecture will provide an introduction to mass spectrometry (MS) based proteomics analysis. Slides created by Melanie Föll.
Length: 20 minutes
Captions: Melanie Föll
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
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Speaker

Tutorial Video

Description:

Modern mass spectrometry-based proteomics enables the identification and quantification of thousands of proteins. Therefore, quantitative mass spectrometry represents an indispensable technology for biological and clinical research. Statistical analyses are required for the unbiased answering of scientific questions and to uncover all important information in the proteomic data. In this training we will cover the full analysis workflow from label-free, data dependent acquisition (DDA) raw data to statistical results. We’ll use two popular quantitative proteomics software: MaxQuant and MSstats.
Length: 1 hour
Captions: Melanie Föll
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn how to use MaxQuant and MSstats for the analysis of label-free shotgun (DDA) data
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Speaker

Friday: Microbiome

To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene is often used. This allows us to identify the bacterial species present in our sample. This lecture and practical session introduces you to 16S analysis in Galaxy using the mothur tool suite.

metagenomics/introduction/slides (Lecture)

Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

metagenomics/mothur-miseq-sop-short/tutorial (Tutorial)

Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
Length: 1 hour 37 minutes
Captions: Saskia Hiltemann
Created: 19 May 2023
Materials:
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Speaker

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In this 3-part module, you will learn about Nanopore long-read sequencing for the detection of antimicrobial resistance (AMR). There is a short video showing you the wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, and finally a practical tutorial walking you through an AMR analysis in Galaxy.

MinION Wetlab demo (Demo)

Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Support:
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Speaker

Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)

Description:

Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.
Length: 30 minutes
Captions: Helena Rasche
Created: 15 February 2021
Support:
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Speaker

metagenomics/plasmid-metagenomics-nanopore/tutorial (Tutorial)

Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.
Length: 45 minutes
Captions: Bérénice Batut
Created: 15 February 2021
Materials:
Support:
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Speaker

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