Module: Genomics
This modules covers the basics of sequence analysis, including Quality Control (QC), mapping, and genome assembly.
Introduction to Genome analysis
These videos cover the most common steps in -omics analysis; Quality control, followed by either mapping or assembly, depending on the availability of a reference genome.
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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Tutorial:
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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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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Tutorial Video
| Description: | In this tutorial, we will walk you through an assembly of a large genome, such as a plant or animal genome. |
| Length: | 25 minutes |
| Captions: | Anna Syme |
| Created: | 16 May 2023 |
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Advanced Genomics Analyses
After data cleaning, we can move on to the core of our analysis, depending on our analysis question. Below are some examples of such genome analyses.
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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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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