Microbial data analysis in Galaxy

Whether you are analysing 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!

microGalaxy is a community of practice in the Galaxy community for anything regarding microbial data analysis in Galaxy!

What is available?


Many tools for microbial data analysis are freely available in the ToolShed which can be installed on any Galaxy server. To keep an overview, the microGalaxy community of practice maintains a curated list of the 200+ tools available.

If tools are missing or information is not up-to-date in the list, please help us! Contact Saskia, Paul or Bérénice about it.

microGalaxy tools

The wordcloud is based on the number of users that used the shown tools since beginning of 2022 until Sept. 2023. The usage numbers were queried from useglaxy.eu and the tools comprise all dedicated tools selected for this community.

Workflows and tutorials

Several curated Galaxy workflows are publicly available for different kinds of microbial data analysis. Many of these are accompanied by comprehensive GTN Tutorials that will guide you through the analysis step by step.

The lists below are far from being exhaustive and up-to-date. Something missing? Feel free to update the page or reach to us


Target Technique Sequencing Analysis GTN Tutorial Workflow Notes
Bacteria 16S Short reads Taxonomic Profiling mothur SOP
Bacteria 16S Long reads Taxonomic Profiling
Bacteria, Fungi SSU, LSU and ITS Short reads Taxonomic Profiling and Visualization WIP WIP Amplicon part of MGnify v5
All Shotgun metagenomics Short reads Taxonomic Profiling, Functional Analysis ASaiM Docs
Plasmid Shotgun metagenomics Long reads AMR detection
Beer microbiome Shotgun metagenomics Long reads Taxonomic profiling
All Shotgun metatranscriptomics Short reads Functional Analysis ASaiM-MT
Pathogens Shotgun metagenomics Long reads Taxonomic Profiling, Gene Identification, SNP identification, Pathogen Tracking
All Shotgun metagenomics Short reads Assembly
All Shotgun metagenomics Short reads Taxonomic Profiling and Visualization
Bacteria Shotgun metagenomics, metatranscriptomics, metaproteomics Short reads MAGs builing, Functional analysis, Multiomics analysis NA ViMO (Visualizer for Meta-Omics)

Bacterial Isolates

Target Sequencing Analysis GTN Tutorial Workflow Notes
M. tuberculosis Short reads Variant Detection
M. tuberculosis Short reads Transmission of Mtb
M. tuberculosis Short reads Phylogenetics applied to Mtb evolution & epidemiology
Plasmids Long reads AMR detection

Want to include your workflow here? Let us know!

A dedicated interface

A dedicated interface with tools, workflows for microbial data analyses can be accessed via microgalaxy.usegalaxy.eu

Training material and events

The Galaxy community organizes regularly training events. You can check the event pages here to get the last ones.

We would like to highlight few events related to microbial data analysis:

How is Galaxy used for microbial data analysis?

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 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

microGalaxy Community

Logo for microgalaxy

microGalaxy is a community of practice to

  • Develop and Sustain microbial data analysis in Galaxy
  • Implement standardised "best practices"
  • Expand documentation and training
  • Coordinate efforts to avoid redundancy in tools, workflows and training
  • Share the amazing things we are all doing together and outside Galaxy
  • Support each other


The microGalaxy community usually meets 4 times per year (including 1 BoF at GCC and other community events) for a 2-hour meeting. The meeting time alternates between 5-7pm Central European time and 9-11am Central European time in order to support members leaving in different timezones. The main aims of the meetings are to

  • Get news and updates from the community
  • Have 1 or more "short" talks about a project or a topic of interest
  • Discuss and coordinate our efforts.

Details about the next events and minutes of previous meetings can be found here.

Working groups

2 working groups were started within the community to work together towards the goals of the commmunity:

  • A Tool working groups with the aims to

    • Create and maintain a curated up-to-date list of the available tools in Galaxy ecosystem for microbial data analysis
    • Create a wishlist of tools to integrate in Galaxy
    • Assess the needs from users for tools in Galaxy
    • Organise hackathons to add tools in connection with the global community
  • A Paper(s) working groups with the aims to

    • Advertise about microbial data analysis in Galaxy
    • Investigate on the uses of Galaxy for microbial data analysis
    • Aggregate information about available resources and infrastructure within Galaxy community
    • Reflect on a roadmap for the community

Join us

Anybody interested in microbial data analysis in the Galaxy is welcome to join microGalaxy! Everybody is Welcome!