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
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
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:

orcid logoFabio Cumbo avatar Fabio Cumboorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnna Syme avatar Anna SymeSophia Hampe avatar Sophia Hampeorcid logoNadia Goué avatar Nadia Gouéorcid logoBjörn Grüning avatar Björn Grüningorcid logoRand Zoabi avatar Rand Zoabiorcid logoWolfgang Maier avatar Wolfgang MaierSantino Faack avatar Santino Faackorcid logoVini Salazar avatar Vini Salazarorcid logoHelena Rasche avatar Helena Rascheorcid logoLinelle Abueg avatar Linelle AbuegWilliam Durand avatar William Durandorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoNicola Soranzo avatar Nicola SoranzoBethan Manley avatar Bethan Manleyorcid logoSubina Mehta avatar Subina Mehtaorcid logoDaniel Blankenberg avatar Daniel BlankenbergKatherine Do avatar Katherine Doorcid logoEngy Nasr avatar Engy Nasrorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoPaul Zierep avatar Paul ZierepIgor Makunin avatar Igor MakuninTarnima Omara avatar Tarnima OmaraWillem de Koning avatar Willem de Koningorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoDeepti Varshney avatar Deepti VarshneyNiall Beard avatar Niall BeardEmma Leith avatar Emma LeithMatthias Bernt avatar Matthias Berntorcid logoClea Siguret avatar Clea Siguretorcid logoTimothy J. Griffin avatar Timothy J. GriffinChristine Oger avatar Christine Ogerorcid logoDave Clements avatar Dave ClementsNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoCristóbal Gallardo avatar Cristóbal GallardoPraveen Kumar avatar Praveen Kumarorcid logoArmin Dadras avatar Armin DadrasRay Sajulga avatar Ray Sajulgaorcid logoTeresa Müller avatar Teresa Müllerorcid logoPolina Polunina avatar Polina PoluninaMichael Thang avatar Michael Thangorcid logoPratik Jagtap avatar Pratik JagtapNuwan Goonasekera avatar Nuwan GoonasekeraDidier Debroas avatar Didier Debroasorcid logoBérénice Batut avatar Bérénice BatutSujai Kumar avatar Sujai KumarSiyu Chen avatar Siyu ChenDechen Bhuming avatar Dechen Bhuming

Funding

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

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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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Melbourne Bioinformatics
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ELIXIR Europe
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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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IFB
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Australian BioCommons
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The University of Melbourne
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de.KCD
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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.