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
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
Metabarcoding of bacteria in dunnart faecal samples across Australia (wild + captive) using QIIME 2
qiime2 taxonomy metabarcoding amplicon microbiome
Metabarcoding of bacteria in dunnart faecal samples across Australia (wild + captive) using QIIME 2
qiime2 taxonomy metabarcoding amplicon microbiome
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:

Ray Sajulga avatar Ray Sajulgaorcid logoXenia Morera Martínez avatar Xenia Morera Martínezorcid logoAnna Syme avatar Anna Symeorcid logoLaura Geissler avatar Laura Geisslerorcid logoFabio Cumbo avatar Fabio Cumboorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoClea Siguret avatar Clea SiguretPraveen Kumar avatar Praveen Kumarorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoSantino Faack avatar Santino FaackEmma Gail avatar Emma Gailorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoRand Zoabi avatar Rand Zoabiorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMatthias Bernt avatar Matthias Berntorcid logoBjörn Grüning avatar Björn Grüningorcid logoPaul Zierep avatar Paul ZierepDidier Debroas avatar Didier Debroasorcid logoSubina Mehta avatar Subina MehtaBethan Manley avatar Bethan Manleyorcid logoPolina Polunina avatar Polina Poluninaorcid logoVini Salazar avatar Vini Salazarorcid logoEngy Nasr avatar Engy NasrChristine Oger avatar Christine Ogerorcid logoLinelle Abueg avatar Linelle Abuegorcid logoWolfgang Maier avatar Wolfgang MaierSujai Kumar avatar Sujai Kumarorcid logoTeresa Müller avatar Teresa Müllerorcid logoArmin Dadras avatar Armin DadrasEmma Leith avatar Emma Leithorcid logoBérénice Batut avatar Bérénice Batutorcid logoGayle Philip avatar Gayle Philiporcid logoNadia Goué avatar Nadia GouéIgor Makunin avatar Igor MakuninSophia Hampe avatar Sophia Hampeorcid logoGiuseppe Defazio avatar Giuseppe DefazioMichael Thang avatar Michael Thangorcid logoAshley Dungan avatar Ashley DunganNiall Beard avatar Niall Beardorcid logoTristan Reynolds avatar Tristan ReynoldsSiyu Chen avatar Siyu Chenorcid logoHelena Rasche avatar Helena Rascheorcid logoDave Clements avatar Dave Clementsorcid logoBert Droesbeke avatar Bert DroesbekeTarnima Omara avatar Tarnima OmaraWilliam Durand avatar William DurandNuwan Goonasekera avatar Nuwan GoonasekeraWillem de Koning avatar Willem de KoningNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoDeepti Varshney avatar Deepti Varshney

Funding

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

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de.KCD
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The University of Melbourne
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Australian BioCommons
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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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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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Melbourne Bioinformatics
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ELIXIR Europe
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EOSC-Life
EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087