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 logoPratik Jagtap avatar Pratik JagtapKatherine Do avatar Katherine Doorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBjörn Grüning avatar Björn Grüningorcid logoTeresa Müller avatar Teresa Müllerorcid logoGiuseppe Defazio avatar Giuseppe Defazioorcid logoBert Droesbeke avatar Bert DroesbekeBethan Manley avatar Bethan ManleySiyu Chen avatar Siyu Chenorcid logoPaul Zierep avatar Paul ZierepTarnima Omara avatar Tarnima Omaraorcid logoRand Zoabi avatar Rand ZoabiEmma Leith avatar Emma LeithWillem de Koning avatar Willem de KoningSophia Hampe avatar Sophia Hampeorcid logoEngy Nasr avatar Engy Nasrorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoArmin Dadras avatar Armin Dadrasorcid logoSaskia Hiltemann avatar Saskia HiltemannWilliam Durand avatar William Durandorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoSubina Mehta avatar Subina MehtaChristine Oger avatar Christine Ogerorcid logoHelena Rasche avatar Helena Rascheorcid logoNadia Goué avatar Nadia GouéNiall Beard avatar Niall Beardorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoClea Siguret avatar Clea SiguretIgor Makunin avatar Igor Makuninorcid logoNikos Pechlivanis avatar Nikos PechlivanisDidier Debroas avatar Didier Debroasorcid logoDave Clements avatar Dave Clementsorcid logoVini Salazar avatar Vini SalazarNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoBérénice Batut avatar Bérénice Batutorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoDaniel Blankenberg avatar Daniel BlankenbergNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoSantino Faack avatar Santino FaackRay Sajulga avatar Ray Sajulgaorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoPolina Polunina avatar Polina PoluninaPraveen Kumar avatar Praveen KumarMatthias Bernt avatar Matthias BerntSujai Kumar avatar Sujai Kumarorcid logoAnna Syme avatar Anna Symeorcid logoFabio Cumbo avatar Fabio CumboDechen Bhuming avatar Dechen BhumingMichael Thang avatar Michael Thang

Funding

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

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IFB
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Australian BioCommons
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ELIXIR Europe
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de.KCD
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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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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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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.