Welcome to microGalaxy!
Whether you are analyzing microbiome samples or bacterial isolates, long reads or short, shotgun or 16S, genomics, transcriptomics, proteomics or metabolomics, multiomics or integrative analysis this is the place to be!
Content
Join the μGalaxy Community
Anybody interested in microbiology in Galaxy is welcome to join our microGalaxy interest group! Everybody is Welcome!
- Join the Discussion! Gitter Chat (also available via Matrix)
- Join our quarterly meetings! Agenda and minutes
Training
Want to learn even more about microbial analysis? You can check out our various microbial dedicated training page within the wider Galaxy Training Network.
- Metagenomic learning paths
- Metabolomics
- Genome Annotation
- Tuberculosis evolution
- Microbial Variant Calling
Galaxy Training Network Tutorials tagged with #microGalaxy
Workflows
Below are a list of curated Galaxy workflows for different kinds of microbial analysis. Many of these are accompanied by comprehensive GTN Tutorials that will guide you through the analysis step by step.
Want to include your workflow here? All you need to do is to make your workflow publicly available via usegalaxy.eu/.org/.org.au. (or any of the subdomains) and tag the workflow with #microGalaxy.
MicroGalaxy Workflows
Tools
More than 200 tools are available for microbiome data analysis in this custom Galaxy instance, major tools to highlight are:
- General tools
- Data retrieval: EBISearch, ENASearch, SRA Tools
- BAM/SAM file manipulation: SAM tools
- BIOM file manipulation: BIOM-Format tools
- Genomics tools
- Quality control: FastQC, PRINSEQ, Cutadapt, fastp, Trimmomatic, MultiQC
- Clustering: CD-Hit
- Sorting and prediction: SortMeRNA, FragGeneScan
- Mapping: BWA, Bowtie
- Similarity search: NCBI Blast+, Diamond
- Alignment: HMMER3
- Microbiota dedicated tools
- Microbial: Scoary, Prokka, Roary
- Metagenomics data manipulation: VSearch, Nonpareil, DADA2
- Assembly: MEGAHIT, metaSPAdes, metaQUAST, VALET, Bandage, MaxBin2
- Metataxonomic sequence analysis: Mothur, QIIME, Vegan
- Taxonomy assignation: MetaPhlAn, Kraken, CAT/BAT
- Metabolism assignation: HUMAnN, PICRUST, InterProScan
- Visualization: Export2graphlan, GraPhlAn, KRONA
- Metaproteomics: MaxQuant, SearchGUI, PeptideShaker, Unipept
Curated community tool list
The complete curated list of all the tools is weekly updated and available here:
Want to know how this list is created and maintained have a look at the dedicated GitHub project. If tools are missing or information is not up-to-date in the list, please help us! Contact Saskia, Paul or Bérénice about it.
Projects
Below is a list of projects that members of this community are involved in (feel free to add your own!)
Projects / Showcases
Below is a list of projects involving members of this community:
| Project | Description | Techniques | Sequencing | Analyses | People involved | Funding | Status |
|---|---|---|---|---|---|---|---|
| IRIDA | The Integrated Rapid Infectious Disease Analysis | Aaron Petkau | |||||
| Foodborne pathogen detection | Metagenomics | Long reads | Bérénice Batut, Engy Nasr | EOSC-Life for 2022 | Ongoing | ||
| BeerDEcoded | General public education project | Metagenomics | Long reads | Bérénice Batut, Street Science Community | Mozilla, de.NBI | Ongoing | |
| DNAnalyzer | Online & interactive game on DNA data analysis | Metagenomics | Long reads | Bérénice Batut, Street Science Community | University of Freiburg | Ongoing | |
| Cloud data | Metagenomics, metatranscriptomics | Short reads | Taxonomy profiling, Functional profiling, Assembly, MAGs builiding | Bérénice Batut, Engy Nasr | Ongoing | ||
| ASaiM | Metagenomics, metatranscriptomics | Short reads | Taxonomy profiling, Functional profiling | Bérénice Batut, Saskia Hilteman, Pratik Jagtap, Subina Mehta, etc | Finished? | ||
| Mycobacterium tuberculosis NGS made easy: data | Series of modules containing recorded videos by experts and tutorials | Illumina (wanting to expand to nanopore) | Mapping & Variant calling, Molecular epidemiology of TB using NGS, Phylogenetics for studying TB evolution and epidemiology | Daniela Brites, Peter van Heusden, Galo A. Goig, Christoph Stritt | Initially funded trough TB projects of capacity building; currently no funding | Ready to be used but also working on improvements |
Partners
| Partners | Description | People involved |
|---|---|---|
| Seq4AMR | JPIAMR Network for Integrating Microbial Sequencing and Platforms for Antimicrobial Resistance | Saskia Hilteman |
| ELIXIR Emerging Microbiome Community | Bérénice Batut | |
| µbioinfo Slack | microbial-bioinfo |
If you would like to know more about any of these projects or get involved, please contact us on the microGalaxy Gitter channel.
Resources
| Resource | Description | Links |
|---|---|---|
 | JPIAMR: Global Coordination of Antimicrobial Resistance Research | Website |
Our Data Policy
| Registered Users | Unregistered Users | FTP Data | GDPR Compliance |
|---|---|---|---|
| For all different storage options, for detailed explanations of data retention policies, and ways how to increase your quota please refer to our dedicated storage site. | Processed data will only be accessible during one browser session, using a cookie to identify your data. This cookie is not used for any other purposes (e.g. tracking or analytics). If UseGalaxy.eu service is not accessed for 90 days, those datasets will be permanently deleted. | Any user data uploaded to our FTP server should be imported into Galaxy as soon as possible. Data left in FTP folders for more than 3 months, will be deleted. | The Galaxy service complies with the EU General Data Protection Regulation (GDPR). You can read more about this on our Terms and Conditions. |