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:

William Durand avatar William DurandDidier Debroas avatar Didier Debroasorcid logoDave Clements avatar Dave Clementsorcid logoClea Siguret avatar Clea SiguretNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoArmin Dadras avatar Armin Dadrasorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoFabio Cumbo avatar Fabio Cumboorcid logoNadia Goué avatar Nadia GouéSujai Kumar avatar Sujai Kumarorcid logoPolina Polunina avatar Polina Poluninaorcid logoHelena Rasche avatar Helena RascheNatalie Whitaker-Allen avatar Natalie Whitaker-AllenEmma Leith avatar Emma LeithBethan Manley avatar Bethan Manleyorcid logoTeresa Müller avatar Teresa MüllerChristine Oger avatar Christine OgerDechen Bhuming avatar Dechen Bhumingorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosSiyu Chen avatar Siyu Chenorcid logoDaniel Blankenberg avatar Daniel BlankenbergIgor Makunin avatar Igor Makuninorcid logoBjörn Grüning avatar Björn GrüningMichael Thang avatar Michael ThangPraveen Kumar avatar Praveen Kumarorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal GallardoRay Sajulga avatar Ray SajulgaKatherine Do avatar Katherine Doorcid logoVini Salazar avatar Vini SalazarMatthias Bernt avatar Matthias Berntorcid logoLinelle Abueg avatar Linelle Abuegorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzSophia Hampe avatar Sophia HampeTarnima Omara avatar Tarnima Omaraorcid logoRand Zoabi avatar Rand Zoabiorcid logoPratik Jagtap avatar Pratik JagtapWillem de Koning avatar Willem de KoningNiall Beard avatar Niall Beardorcid logoPaul Zierep avatar Paul Ziereporcid logoSantino Faack avatar Santino Faackorcid logoGiuseppe Defazio avatar Giuseppe Defazioorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoAnna Syme avatar Anna Symeorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoEngy Nasr avatar Engy Nasrorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoSubina Mehta avatar Subina Mehtaorcid logoMina Hojat Ansari avatar Mina Hojat Ansari

Funding

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

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