Microbiome — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

orcid logoPaul Zierep avatar Paul Ziereporcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBérénice Batut avatar Bérénice Batut

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
Sufficient Editorial Board Members Done ✅ (3 members) Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Done ✅ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Done ✅ (3 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
Learning Pathway CTA Done ✅ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.

Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to Microbiome Analysis ❌ ❌ ❌ ✅ ❌
Analyses of metagenomics data - The global picture ❌ ❌ ❌ ✅ ❌
16S Microbial analysis with Nanopore data ❌ ❌ ❌ ✅ ❌
Antibiotic resistance detection ❌ ❌ ❌ ✅ ❌
Building an amplicon sequence variant (ASV) table from 16S data using DADA2 ✅ ❌ ❌ ✅ ❌
QIIME 2 Cancer Microbiome Intervention ✅ ❌ ❌ ✅ ❌
QIIME 2 Moving Pictures ✅ ❌ ❌ ✅ ❌
16S Microbial Analysis with mothur (extended) ❌ ❌ ❌ ✅ ❌
16S Microbial Analysis with mothur (short) ❌ ❌ ❌ ✅ ❌
Assembly of metagenomic sequencing data ✅ ❌ ❌ ✅ ❌
Binning of metagenomic sequencing data ✅ ❌ ❌ ✅ ❌
Calculating α and β diversity from microbiome taxonomic data ✅ ❌ ❌ ✅ ❌
Identification of the micro-organisms in a beer using Nanopore sequencing ✅ ❌ ❌ ✅ ❌
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition ✅ ❌ ❌ ✅ ❌
Taxonomic Profiling and Visualization of Metagenomic Data ✅ ❌ ❌ ✅ ❌
Metatranscriptomics analysis using microbiome RNA-seq data ❌ ❌ ❌ ✅ ❌
Metatranscriptomics analysis using microbiome RNA-seq data (short) ❌ ❌ ❌ ✅ ❌
Clinical Metaproteiomics 1: Database-Generation ✅ ✅ ✅ ✅ ❌
Clinical Metaproteomics 2: Discovery ✅ ✅ ✅ ✅ ❌
Clinical Metaproteomics 3: Verification ✅ ✅ ✅ ✅ ❌
Clinical Metaproteomics 4: Quantitation ✅ ✅ ✅ ✅ ❌
Clinical Metaproteomics 5: Data Interpretation ✅ ✅ ✅ ✅ ❌
Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 ✅ ✅ ❌ ✅ ❌

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Analyses of metagenomics data - The global picture Amplicon Tutorial Jan 6, 2025 1 ✅ ❌ ❌
Analyses of metagenomics data - The global picture WGS Part In "Analyses Of Metagenomics Data - The Global Picture" Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial analysis with Nanopore data Training: 16S rRNA Analysis with Nanopore Sequencing Reads Jan 6, 2025 1 ❌ ❌ ❌
Antibiotic resistance detection Copy Of GTN Training - Antibiotic Resistance Detection Jan 6, 2025 1 ❌ ❌ ❌
Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Jan 6, 2025 1 ✅ ❌ ❌
16S Microbial Analysis with mothur (extended) Training: 16S rRNA Sequencing With Mothur: Main Tutorial Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial Analysis with mothur (short) Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial Analysis with mothur (short) Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial Analysis with mothur (short) Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial Analysis with mothur (short) Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial Analysis with mothur (short) Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial Analysis with mothur (short) Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] Jan 6, 2025 1 ❌ ❌ ❌
16S Microbial Analysis with mothur (short) Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] Jan 6, 2025 1 ❌ ❌ ❌
Assembly of metagenomic sequencing data Metagenomics assembly tutorial workflow Jan 6, 2025 1 ❌ ❌ ❌
Assembly of metagenomic sequencing data workflow-generate-dataset-for-assembly-tutorial Jan 6, 2025 1 ❌ ❌ ❌
Calculating α and β diversity from microbiome taxonomic data Calculating diversity from microbiome taxonomic data Jan 6, 2025 1 ✅ ✅ ❌
Identification of the micro-organisms in a beer using Nanopore sequencing Identification of the micro-organisms in a beer using Nanopore sequencing Jan 6, 2025 1 ✅ ❌ ❌
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Allele-based Pathogen Identification Jan 6, 2025 1 ✅ ✅ ✅
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Gene-based Pathogen Identification Jan 6, 2025 2 ✅ ✅ ✅
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Nanopore Preprocessing Jan 6, 2025 3 ✅ ✅ ✅
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation Jan 6, 2025 2 ❌ ✅ ✅
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Taxonomy Profiling and Visualization with Krona Jan 6, 2025 2 ✅ ✅ ✅
Taxonomic Profiling and Visualization of Metagenomic Data Taxonomic Profiling and Visualization of Metagenomic Data Jan 6, 2025 1 ✅ ❌ ❌
Metatranscriptomics analysis using microbiome RNA-seq data Main Metatranscriptomics Analysis Jan 6, 2025 1 ✅ ❌ ❌
Metatranscriptomics analysis using microbiome RNA-seq data (short) Workflow 1: Preprocessing Jan 6, 2025 1 ✅ ❌ ❌
Metatranscriptomics analysis using microbiome RNA-seq data (short) Workflow 2: Community Profile Jan 6, 2025 1 ✅ ❌ ❌
Metatranscriptomics analysis using microbiome RNA-seq data (short) Workflow 3: Functional Information Jan 6, 2025 1 ✅ ❌ ❌
Metatranscriptomics analysis using microbiome RNA-seq data (short) Workflow 3: Functional Information (quick) Jan 6, 2025 1 ✅ ❌ ❌
Clinical Metaproteiomics 1: Database-Generation WF1_Database_Generation_Workflow Jan 6, 2025 0 ❌ ❌ ❌
Clinical Metaproteomics 2: Discovery WF2_Discovery-Workflow Jan 6, 2025 0 ❌ ❌ ❌
Clinical Metaproteomics 3: Verification WF3_VERIFICATION_WORKFLOW Jan 6, 2025 0 ❌ ❌ ❌
Clinical Metaproteomics 4: Quantitation WF4_Quantitation_Workflow Jan 6, 2025 0 ❌ ❌ ❌
Clinical Metaproteomics 5: Data Interpretation WF5_Data_Interpretation_Worklow Jan 6, 2025 0 ❌ ❌ ❌
Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' Jan 6, 2025 1 ✅ ✅ ❌

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Learning Pathways using materials from this Topic

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Detection of AMR genes in bacterial genomes

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

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Metagenomics data processing and analysis for microbiome

This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications

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