Assembly

Lesson Slides Hands-on Recordings Input dataset Workflows
Assembly of metagenomic sequencing data
assembly metagenomics microgalaxy
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
nanopore assembly amr microgalaxy
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
illumina assembly microgalaxy
Making sense of a newly assembled genome
gmod prokaryote microgalaxy jbrowse1
Unicycler Assembly
prokaryote microgalaxy

Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
Checking expected species and contamination in bacterial isolate
illumina bacteria microgalaxy

Evolution

Lesson Slides Hands-on Recordings Input dataset Workflows
Identifying tuberculosis transmission links: from SNPs to transmission clusters
prokaryote one-health microgalaxy
Tree thinking for tuberculosis evolution and epidemiology
prokaryote one-health phylogenetics microgalaxy

Genome Annotation

Lesson Slides Hands-on Recordings Input dataset Workflows
Bacterial Genome Annotation
gmod illumina bacteria microgalaxy jbrowse1
Genome annotation with Prokka
gmod prokaryote microgalaxy jbrowse1
Identification of AMR genes in an assembled bacterial genome
gmod illumina amr one-health jbrowse1 microgalaxy
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 apollo2
Comparative gene analysis in unannotated genomes
evolution annotation vgp cookbook eukaryote prokaryote microgalaxy
Essential genes detection with Transposon insertion sequencing
bacteria tnseq essential genes microgalaxy

Microbiome

Lesson Slides Hands-on Recordings Input dataset Workflows
16S Microbial analysis with Nanopore data
metabarcoding 16S nanopore microgalaxy plants
Analyses of metagenomics data - The global picture
microgalaxy
Antibiotic resistance detection
nanopore plasmids assembly amr microgalaxy
Assembly of metagenomic sequencing data
assembly metagenomics microgalaxy
Binning of metagenomic sequencing data
binning metagenomics microgalaxy
Building an amplicon sequence variant (ASV) table from 16S data using DADA2
metabarcoding 16S microgalaxy
Identification of the micro-organisms in a beer using Nanopore sequencing
nanopore beer citizen science metagenomics microgalaxy
Metatranscriptomics analysis using microbiome RNA-seq data
metatranscriptomics microgalaxy
Metatranscriptomics analysis using microbiome RNA-seq data (short)
metatranscriptomics microgalaxy
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
microgalaxy Nanopore data analysis Pathogens detection Phylogenetic tree Heatmap cyoa
QIIME 2 Cancer Microbiome Intervention
metabarcoding 16S taxonomic profiling diversity microgalaxy
QIIME 2 Moving Pictures
metagenomics taxonomic profiling diversity microgalaxy
Taxonomic Profiling and Visualization of Metagenomic Data
metagenomics taxonomic profiling microgalaxy
16S Microbial Analysis with mothur (extended)
metabarcoding 16S microgalaxy
16S Microbial Analysis with mothur (short)
metabarcoding 16S microgalaxy

Proteomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Metaproteomics tutorial
microgalaxy
metaQuantome 1: Data creation
microgalaxy
metaQuantome 2: Function
microgalaxy
metaQuantome 3: Taxonomy
microgalaxy

Sequence analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Quality and contamination control in bacterial isolate using Illumina MiSeq Data
illumina bacteria microgalaxy

Variant Analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Calling variants in non-diploid systems
prokaryote microgalaxy
M. tuberculosis Variant Analysis
prokaryote one-health microgalaxy tuberculosis
Microbial Variant Calling
prokaryote microgalaxy gmod jbrowse1