Module: Bioinformatics Buffet
This module will cover the introductory materials of a broad range of topics in bioinformatics.
Monday: Introduction to Galaxy and Genomics
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 |
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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 |
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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 |
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| Supported Servers: | Known Working Possibly Working |
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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 |
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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 |
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| Supported Servers: | Known Working Possibly Working |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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| Supported Servers: | Known Working Possibly Working |
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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 |
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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 |
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| Supported Servers: | Known Working Possibly Working |
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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 |
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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 |
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| Supported Servers: | Known Working Possibly Working |
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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 |
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| Supported Servers: | Known Working Possibly Working |
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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 |
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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 |
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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.
Introduction to Microbiome Analysis (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 |
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16S Microbial Analysis with mothur (short) (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 |
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| Supported Servers: | Known Working Possibly Working |
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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.
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Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)
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Antibiotic resistance detection (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 |
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