microbiome

Tutorials covering microbiome

Material

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

Microbiome

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Microbiome Analysis
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
Calculating α and β diversity from microbiome taxonomic data
metagenomics diversity
Clinical Metaproteomics 1: Database-Generation
label-TMT11
Clinical Metaproteomics 2: Discovery
label-TMT11
Clinical Metaproteomics 3: Verification
label-TMT11
Clinical Metaproteomics 4: Quantitation
label-TMT11
Clinical Metaproteomics 5: Data Interpretation
label-TMT11
Detection of shared microbial strains with SameStr
metagenomics microbiome microgalaxy
Detection of shared microbial strains with SameStr
metagenomics microbiome microgalaxy
Identification of the micro-organisms in a beer using Nanopore sequencing
nanopore beer citizen science metagenomics microgalaxy
Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2
fungi ecology
Indexing and profiling microbes with MetaSBT
metagenomics diversity taxonomic profiling
MGnify v5.0 Amplicon Pipeline
microbiome amplicon taxonomy taxonomic abundance
MGnify v5.0 Amplicon Pipeline
microbiome amplicon taxonomy taxonomic abundance
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
Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data
Remove contamination and host reads
host-removal preprocessing metagenomics 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

Contributors

This material was contributed to by:

Natalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoLinelle Abueg avatar Linelle AbuegSujai Kumar avatar Sujai Kumarorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoNadia Goué avatar Nadia Gouéorcid logoDeepti Varshney avatar Deepti VarshneySophia Hampe avatar Sophia Hampeorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoGiuseppe Defazio avatar Giuseppe DefazioSiyu Chen avatar Siyu Chenorcid logoBérénice Batut avatar Bérénice Batutorcid logoPolina Polunina avatar Polina PoluninaIgor Makunin avatar Igor Makuninorcid logoPaul Zierep avatar Paul Ziereporcid logoVini Salazar avatar Vini SalazarWilliam Durand avatar William DurandWillem de Koning avatar Willem de Koningorcid logoBjörn Grüning avatar Björn GrüningRay Sajulga avatar Ray Sajulgaorcid logoMatthias Bernt avatar Matthias Berntorcid logoHelena Rasche avatar Helena Rascheorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoEngy Nasr avatar Engy Nasrorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoArmin Dadras avatar Armin Dadrasorcid logoTeresa Müller avatar Teresa MüllerNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosDidier Debroas avatar Didier Debroasorcid logoClea Siguret avatar Clea Siguretorcid logoDaniel Blankenberg avatar Daniel BlankenbergMichael Thang avatar Michael ThangNiall Beard avatar Niall Beardorcid logoSubina Mehta avatar Subina MehtaBethan Manley avatar Bethan ManleyKatherine Do avatar Katherine Doorcid logoAnna Syme avatar Anna Symeorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoRand Zoabi avatar Rand Zoabiorcid logoDave Clements avatar Dave ClementsDechen Bhuming avatar Dechen Bhumingorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoSantino Faack avatar Santino Faackorcid logoXenia Morera Martínez avatar Xenia Morera MartínezEmma Leith avatar Emma Leithorcid logoFabio Cumbo avatar Fabio CumboPraveen Kumar avatar Praveen KumarChristine Oger avatar Christine OgerTarnima Omara avatar Tarnima Omaraorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoCristóbal Gallardo avatar Cristóbal Gallardo

Funding

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

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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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The University of Melbourne
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Melbourne Bioinformatics
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ELIXIR Europe
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Australian BioCommons
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SPUN
SPUN is a scientific research organization founded to map mycorrhizal fungal communities and advocate for their protection.
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de.KCD
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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