Module: Microbial Analysis

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

• Slides: Version in Video | Latest Version

• Slack: #metagenomics_introduction
  • Slack Invite
• Gitter
• Galaxy Help Forum

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

• Tutorial: Version in Video | Latest Version
  FAQs

• Slack: #metagenomics_mothur-miseq-sop-short
  • Slack Invite
• Gitter
• Galaxy Help Forum

• Tutorial: Version in Video | Latest Version
  FAQs

• Slack: #metagenomics_taxonomic-profiling
  • Slack Invite
• Gitter
• Galaxy Help Forum

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

• Slack: #wetlab_miseq
  • Slack Invite
• Gitter
• Galaxy Help Forum

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.

• Slack: #metagenomics_clinical-applications
  • Slack Invite
• Gitter
• Galaxy Help Forum

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

• Tutorial: Version in Video | Latest Version
  FAQs
• Related Tutorial: Version in Video | Latest Version

• Slack: #metagenomics_plasmid-metagenomics-nanopore
  • Slack Invite
• Gitter
• Galaxy Help Forum

In this tutorial, we will be presenting a series of Galaxy workflows whose main goals are 1) to agnostically detect pathogens (What exactly is this pathogen and what virulence factors does it carry?) from data extracted directly (without prior cultivation) from a potentially contaminated sample (e.g. food like chicken, beef, etc.) and sequenced using Nanopore, and 2) to compare different samples to trace the possible source of contamination

• Tutorial: Version in Video | Latest Version
  FAQs

• Slack: #metagenomics_pathogen-detection-from-nanopore-foodborne-data
  • Slack Invite
• Gitter
• Galaxy Help Forum

• Tutorial: Version in Video | Latest Version
  FAQs

• Slack: #metagenomics_beer-data-analysis
  • Slack Invite
• Gitter
• Galaxy Help Forum

In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.

• tutorial: Version in Video | Latest Version

• Slack: #metagenomics_metagenomics-assembly
  • Slack Invite
• Gitter
• Galaxy Help Forum

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.

• Slides

• Slack: #variant-analysis_tb-variant-analysis
  • Slack Invite
• Gitter
• Galaxy Help Forum

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.

• Tutorial: Version in Video | Latest Version
  FAQs

• Slack: #variant-analysis_tb-variant-analysis
  • Slack Invite
• Gitter
• Galaxy Help Forum

• How should we filter those variants
• How can we predict drug resistance from those variants
• How do we annotate those variants

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.

• Slides from video
• Related Slides: Version in Video | Latest Version
• Tutorial: Version in Video | Latest Version
  FAQs

• Slack: #metagenomics_metatranscriptomics
  • Slack Invite
• Gitter
• Galaxy Help Forum

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.

• Tutorial: Version in Video | Latest Version
  FAQs

• Slack: #proteomics_metaproteomics
  • Slack Invite
• Gitter
• Galaxy Help Forum

• UseGalaxy.eu ⭐️
• UseGalaxy.no
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️

• UseGalaxy.be

• A taxonomy and functional analysis of metaproteomic mass spectrometry data.