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 logoPaul Zierep avatar Paul Ziereporcid logoDeepti Varshney avatar Deepti Varshneyorcid logoRand Zoabi avatar Rand Zoabiorcid logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia HiltemannNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoHelena Rasche avatar Helena RascheNatalie Whitaker-Allen avatar Natalie Whitaker-AllenSophia Hampe avatar Sophia HampeDidier Debroas avatar Didier Debroasorcid logoCristóbal Gallardo avatar Cristóbal GallardoMatthias Bernt avatar Matthias Berntorcid logoTimothy J. Griffin avatar Timothy J. GriffinChristine Oger avatar Christine Ogerorcid logoTristan Reynolds avatar Tristan ReynoldsPraveen Kumar avatar Praveen Kumarorcid logoPolina Polunina avatar Polina PoluninaWilliam Durand avatar William DurandSiyu Chen avatar Siyu Chenorcid logoBjörn Grüning avatar Björn GrüningRay Sajulga avatar Ray Sajulgaorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoNadia Goué avatar Nadia Gouéorcid logoTeresa Müller avatar Teresa Müllerorcid logoArmin Dadras avatar Armin Dadrasorcid logoSantino Faack avatar Santino Faackorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoWolfgang Maier avatar Wolfgang MaierWillem de Koning avatar Willem de Koningorcid logoClea Siguret avatar Clea Siguretorcid logoNicola Soranzo avatar Nicola SoranzoEmma Leith avatar Emma Leithorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosTarnima Omara avatar Tarnima Omaraorcid logoSubina Mehta avatar Subina Mehtaorcid logoPratik Jagtap avatar Pratik JagtapBethan Manley avatar Bethan ManleyNiall Beard avatar Niall BeardSujai Kumar avatar Sujai KumarKatherine Do avatar Katherine Doorcid logoFabio Cumbo avatar Fabio Cumboorcid logoVini Salazar avatar Vini SalazarMichael Thang avatar Michael Thangorcid logoDave Clements avatar Dave Clementsorcid logoEngy Nasr avatar Engy NasrIgor Makunin avatar Igor Makuninorcid logoLinelle Abueg avatar Linelle Abuegorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzDechen Bhuming avatar Dechen Bhumingorcid logoAnna Syme avatar Anna Syme

Funding

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

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