Microbiome — Community Home
This is a new, experimental "Community Home" for a given topic. It is intended to highlight community contributions over the years to a topic!2024 Year in Review
So many new additions to our community!
2
News
5
Events
1
Learning Pathways
5
Tutorials
4
Recordings
6
Workflows
3
Contributors
News
- 4th Mycobacterium tuberculosis complex NGS made easy
- New Galaxy training: Building an amplicon sequence variant (ASV) table from 16S data using DADA2
Events
- Workshop on high-throughput sequencing data analysis with Galaxy
- Workshop on high-throughput sequencing data analysis with Galaxy
- Galaxy Training Academy 2024
- Mycobacterium tuberculosis complex NGS made easy
- Mycobacterium tuberculosis complex NGS made easy
Learning Pathways
Tutorials
- Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2
- Calculating α and β diversity from microbiome taxonomic data
- Building an amplicon sequence variant (ASV) table from 16S data using DADA2
- QIIME 2 Moving Pictures
- QIIME 2 Cancer Microbiome Intervention
Recordings
- Recording of Building an amplicon sequence variant (ASV) table from 16S data using DADA2
- Recording of Binning of metagenomic sequencing data
- Recording of Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
- Recording of Calculating α and β diversity from microbiome taxonomic data
Workflows
- Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'
- Calculating diversity from microbiome taxonomic data
- Building an amplicon sequence variant (ASV) table from 16S data using DADA2
- Taxonomy Profiling and Visualization with Krona
- Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
- Allele-based Pathogen Identification
Contributors
2023 Year in Review
So many new additions to our community!
1
News
1
Learning Pathways
3
Tutorials
7
Recordings
10
Faqs
4
Workflows
1
Grants
5
Contributors
News
Learning Pathways
Tutorials
- Binning of metagenomic sequencing data
- Taxonomic Profiling and Visualization of Metagenomic Data
- Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Recordings
- Recording of 16S Microbial Analysis with mothur (short)
- Recording of Metatranscriptomics analysis using microbiome RNA-seq data (short)
- Recording of Metatranscriptomics analysis using microbiome RNA-seq data
- Recording of Taxonomic Profiling and Visualization of Metagenomic Data
- Recording of Identification of the micro-organisms in a beer using Nanopore sequencing
- Recording of Assembly of metagenomic sequencing data
- Recording of Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Faqs
- Do the pipelines work with both isolates and direct from raw meat? or only isolate?
- Can we also use this workflow on Illumina raw reads?
- Can we use snippy pipeline instead for the phylogenetic analysis?
- Isn't it awkward to find so many humans sequences there, since we filter for them before?
- Is there a way to filter on the Kalimari database?
- From where can I import other genomes?
- For preprocessing part with host removal: Where do you find the abbreviations for each host species available (e.g. bos is cow, homo is human..)?
- What does `^.*Gallus|Homo|Bos.*$` mean?
- After sequencing with MinKNOW software, we get many fastq files, do these files need to be combined into one file before uploading or is it possible to upload them all at once?
- Kraken2 and the k-mer approach for taxonomy classification
Workflows
- Taxonomic Profiling and Visualization of Metagenomic Data
- Gene-based Pathogen Identification
- Nanopore Preprocessing
- workflow-generate-dataset-for-assembly-tutorial
Grants
Contributors
2022 Year in Review
So many new additions to our community!
2
Tutorials
6
Faqs
2
Workflows
5
Contributors
Tutorials
- Assembly of metagenomic sequencing data
- Identification of the micro-organisms in a beer using Nanopore sequencing
Faqs
- What is Taxonomy?
- The input for a tool is not listed in the dropdown
- Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?
- Can this ASaiM workflow be used for single-end data?
- Can we use the ASaiM-MT workflow on multiple input files at the same time?
- Why do we use FASTQ interlacer and not the FASTQ joiner?
Workflows
- Metagenomics assembly tutorial workflow
- Identification of the micro-organisms in a beer using Nanopore sequencing
Contributors
2021 Year in Review
So many new additions to our community!
5
Recordings
2
Faqs
1
Contributors
Recordings
- Recording of Introduction to Microbiome Analysis
- Recording of 16S Microbial Analysis with mothur (short)
- Recording of Antibiotic resistance detection
- Recording of Metatranscriptomics analysis using microbiome RNA-seq data (short)
- Recording of Metatranscriptomics analysis using microbiome RNA-seq data
Faqs
Contributors
2020 Year in Review
So many new additions to our community!
2
Tutorials
1
Slides
5
Workflows
1
Grants
1
Contributors
Tutorials
- 16S Microbial analysis with Nanopore data
- Metatranscriptomics analysis using microbiome RNA-seq data (short)
Slides
Workflows
- Training: 16S rRNA Analysis with Nanopore Sequencing Reads
- Workflow 3: Functional Information (quick)
- Workflow 3: Functional Information
- Workflow 2: Community Profile
- Workflow 1: Preprocessing
Grants
Contributors
2019 Year in Review
So many new additions to our community!
3
Tutorials
9
Workflows
4
Contributors
Tutorials
- Metatranscriptomics analysis using microbiome RNA-seq data
- Antibiotic resistance detection
- 16S Microbial Analysis with mothur (short)
Workflows
- Main Metatranscriptomics Analysis
- Copy Of GTN Training - Antibiotic Resistance Detection
- Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]
- Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]
- Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]
- Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]
- Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]
- Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]
- Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]
Contributors
2018 Year in Review
So many new additions to our community!
1
Workflows
3
Contributors
2017 Year in Review
So many new additions to our community!
2
Tutorials
1
Slides
2
Workflows
10
Contributors
Tutorials
Slides
Workflows
- WGS Part In "Analyses Of Metagenomics Data - The Global Picture"
- Training: 16S rRNA Sequencing With Mothur: Main Tutorial
Contributors
Cumulative Data as CSV
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