Module: Microbial Analysis

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
Materials:
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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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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 metagenomics (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 40 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
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Learning Objectives:
  • Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
  • Using a mock community to assess the error rate of your sequencing experiment
  • Visualize sample diversity using Krona and Phinch
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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
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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
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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
Materials:
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Learning Objectives:
  • Perform Quality control on your reads
  • Assemble a genome with Minimap2/Miniasm/Racon
  • Determine the structure of the genome(s)
  • Scan for antimicrobial resistance genes with Staramr
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Tutorial Video

Description:

Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated collection of tools to explore and visualize taxonomic and functional information from metatranscriptomic sequences.
Length: 1 hour 30 minutes
Captions: Engy Nasr, Saskia Hiltemann
Created: 15 February 2021
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Demo Video

Description:

In this tutorial, the basic workflow for metaproteomics is described, which includes database search, seeking taxonomy information and functional analysis. Related metaproteomics and functional microbiome tools and GTN tutorials are also mentioned in this tutorial.
Length: 1 hour
Captions: Emma Leith
Created: 15 February 2021
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Learning Objectives:
  • A taxonomy and functional analysis of metaproteomic mass spectrometry data.
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