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
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:

orcid logoFabio Cumbo avatar Fabio Cumboorcid logoMina Hojat Ansari avatar Mina Hojat AnsariDidier Debroas avatar Didier Debroasorcid logoArmin Dadras avatar Armin Dadrasorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoPolina Polunina avatar Polina PoluninaSophia Hampe avatar Sophia HampePraveen Kumar avatar Praveen Kumarorcid logoDave Clements avatar Dave Clementsorcid logoGiuseppe Defazio avatar Giuseppe DefazioIgor Makunin avatar Igor Makuninorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoHelena Rasche avatar Helena RascheKatherine Do avatar Katherine Doorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnna Syme avatar Anna SymeDechen Bhuming avatar Dechen Bhumingorcid logoSantino Faack avatar Santino FaackSujai Kumar avatar Sujai KumarNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSaskia Hiltemann avatar Saskia HiltemannNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoVini Salazar avatar Vini Salazarorcid logoRand Zoabi avatar Rand ZoabiSiyu Chen avatar Siyu Chenorcid logoPaul Zierep avatar Paul ZierepChristine Oger avatar Christine OgerWilliam Durand avatar William Durandorcid logoDeepti Varshney avatar Deepti VarshneyWillem de Koning avatar Willem de Koningorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoSubina Mehta avatar Subina MehtaNiall Beard avatar Niall BeardBethan Manley avatar Bethan Manleyorcid logoNikos Pechlivanis avatar Nikos PechlivanisMatthias Bernt avatar Matthias Berntorcid logoNadia Goué avatar Nadia GouéTarnima Omara avatar Tarnima Omaraorcid logoEngy Nasr avatar Engy NasrMichael Thang avatar Michael Thangorcid logoTeresa Müller avatar Teresa Müllerorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzEmma Leith avatar Emma Leithorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoLinelle Abueg avatar Linelle AbuegRay Sajulga avatar Ray Sajulgaorcid logoBérénice Batut avatar Bérénice Batutorcid logoClea Siguret avatar Clea Siguretorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoBjörn Grüning avatar Björn Grüning

Funding

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

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