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 logoArmin Dadras avatar Armin DadrasNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoSantino Faack avatar Santino Faackorcid logoFabio Cumbo avatar Fabio Cumboorcid logoAnna Syme avatar Anna SymeEmma Leith avatar Emma Leithorcid logoNadia Goué avatar Nadia Gouéorcid logoPaul Zierep avatar Paul ZierepTarnima Omara avatar Tarnima Omaraorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoSubina Mehta avatar Subina MehtaPraveen Kumar avatar Praveen KumarNiall Beard avatar Niall BeardKatherine Do avatar Katherine DoDidier Debroas avatar Didier DebroasNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoHelena Rasche avatar Helena Rascheorcid logoBert Droesbeke avatar Bert DroesbekeDechen Bhuming avatar Dechen Bhumingorcid logoRand Zoabi avatar Rand Zoabiorcid logoLinelle Abueg avatar Linelle AbuegSujai Kumar avatar Sujai Kumarorcid logoClea Siguret avatar Clea SiguretSophia Hampe avatar Sophia HampeRay Sajulga avatar Ray SajulgaMichael Thang avatar Michael Thangorcid logoEngy Nasr avatar Engy Nasrorcid logoNikos Pechlivanis avatar Nikos PechlivanisChristine Oger avatar Christine Ogerorcid logoBjörn Grüning avatar Björn Grüningorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoSaskia Hiltemann avatar Saskia HiltemannWilliam Durand avatar William DurandBethan Manley avatar Bethan Manleyorcid logoGiuseppe Defazio avatar Giuseppe Defazioorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzMatthias Bernt avatar Matthias BerntIgor Makunin avatar Igor MakuninWillem de Koning avatar Willem de Koningorcid logoPolina Polunina avatar Polina PoluninaSiyu Chen avatar Siyu Chenorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoDave Clements avatar Dave Clementsorcid logoBérénice Batut avatar Bérénice Batutorcid logoTeresa Müller avatar Teresa Müllerorcid logoVini Salazar avatar Vini Salazar

Funding

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

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