microgalaxy

Tutorials covering microgalaxy

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

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 biodiversity

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 biodiversity apollo2
Comparative gene analysis in unannotated genomes
evolution annotation vgp cookbook eukaryote prokaryote microgalaxy biodiversity
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
Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads
assembly binning metagenomics 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

Contributors

This material was contributed to by:

Tarnima Omara avatar Tarnima OmaraNathan Dunn avatar Nathan Dunnorcid logoPolina Polunina avatar Polina Poluninaorcid logoDelphine Lariviere avatar Delphine LariviereJames Johnson avatar James Johnsonorcid logoDave Clements avatar Dave Clementsorcid logoWolfgang Maier avatar Wolfgang MaierValentin Loux avatar Valentin Louxorcid logoMaria Doyle avatar Maria DoyleGalo A. Goig avatar Galo A. GoigMélanie Petera avatar Mélanie Peteraorcid logoBjörn Grüning avatar Björn Grüningorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzHélène Chiapello avatar Hélène Chiapelloorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoLucille Delisle avatar Lucille Delisleorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoAnna Syme avatar Anna SymeChristine Oger avatar Christine Ogerorcid logoClemens Blank avatar Clemens Blankorcid logoNicola Soranzo avatar Nicola SoranzoNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSimon Gladman avatar Simon GladmanThoba Lose avatar Thoba Loseorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoVini Salazar avatar Vini Salazarorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoPaul Zierep avatar Paul ZierepMichael Thang avatar Michael Thangorcid logoMateo Boudet avatar Mateo BoudetDaniela Brites avatar Daniela BritesWillem de Koning avatar Willem de KoningNatalie Whitaker-Allen avatar Natalie Whitaker-AllenVerena Moosmann avatar Verena MoosmannMatthias Bernt avatar Matthias Berntorcid logoTristan Reynolds avatar Tristan ReynoldsMarie Crane avatar Marie Craneorcid logoHelena Rasche avatar Helena RascheBazante Sanders avatar Bazante SandersAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoClea Siguret avatar Clea Siguretorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosEnis Afgan avatar Enis AfganGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAlex Ostrovsky avatar Alex OstrovskyRay Sajulga avatar Ray SajulgaSophia Hampe avatar Sophia Hampeorcid logoSantino Faack avatar Santino FaackWilliam Durand avatar William Durandorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoNate Coraor avatar Nate CoraorTorsten Seemann avatar Torsten SeemannEmma Leith avatar Emma Leithorcid logoSubina Mehta avatar Subina MehtaMatúš Kalaš avatar Matúš Kalašorcid logoPeter van Heusden avatar Peter van HeusdenChristoph Stritt avatar Christoph Strittorcid logoArmin Dadras avatar Armin Dadrasorcid logoBérénice Batut avatar Bérénice Batutorcid logoBert Droesbeke avatar Bert DroesbekeSiyu Chen avatar Siyu ChenNiall Beard avatar Niall Beardorcid logoLinelle Abueg avatar Linelle Abuegorcid logoTeresa Müller avatar Teresa MüllerSimon Bray avatar Simon BrayIgor Makunin avatar Igor Makuninorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoEngy Nasr avatar Engy NasrPraveen Kumar avatar Praveen Kumar

Funding

These individuals or organisations provided funding support for the development of this resource

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Avans
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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Melbourne Bioinformatics
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EOSC-Life
EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087
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IFB
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The University of Melbourne
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ABRomics
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ELIXIR Europe
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Australian BioCommons
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.