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


TargetTechniqueSequencingAnalysisGTN TutorialWorkflowNotes
Bacteria16SShort readsTaxonomic Profilingmothur SOP
Bacteria16SLong readsTaxonomic Profiling
Bacteria, FungiSSU, LSU and ITSShort readsTaxonomic Profiling and VisualizationWIPWIPAmplicon part of MGnify v5
AllShotgun metagenomicsShort readsTaxonomic Profiling, Functional AnalysisASaiM Docs
PlasmidShotgun metagenomicsLong readsAMR detection
Beer microbiomeShotgun metagenomicsLong readsTaxonomic profiling
AllShotgun metatranscriptomicsShort readsFunctional AnalysisASaiM-MT
PathogensShotgun metagenomicsLong readsTaxonomic Profiling, Gene Identification, SNP identification, Pathogen Tracking
AllShotgun metagenomicsShort readsAssembly
AllShotgun metagenomicsShort readsTaxonomic Profiling and Visualization
BacteriaShotgun metagenomics, metatranscriptomics, metaproteomicsShort readsMAGs builing, Functional analysis, Multiomics analysisNAViMO (Visualizer for Meta-Omics)

Bacterial Isolates

TargetSequencingAnalysisGTN TutorialWorkflowNotes
M. tuberculosisShort readsVariant Detection
M. tuberculosisShort readsTransmission of Mtb
M. tuberculosisShort readsPhylogenetics applied to Mtb evolution & epidemiology
PlasmidsLong readsAMR 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:

ProjectDescriptionTechniquesSequencingAnalysesPeople involvedFundingStatus
IRIDAThe Integrated Rapid Infectious Disease AnalysisAaron Petkau
Foodborne pathogen detectionMetagenomicsLong readsBérénice Batut, Engy NasrEOSC-Life for 2022Ongoing
BeerDEcodedGeneral public education projectMetagenomicsLong readsBérénice Batut, Street Science CommunityMozilla, de.NBIOngoing
DNAnalyzerOnline & interactive game on DNA data analysisMetagenomicsLong readsBérénice Batut, Street Science CommunityUniversity of FreiburgOngoing
Cloud dataMetagenomics, metatranscriptomicsShort readsTaxonomy profiling, Functional profiling, Assembly, MAGs builidingBérénice Batut, Engy NasrOngoing
ASaiMMetagenomics, metatranscriptomicsShort readsTaxonomy profiling, Functional profilingBérénice Batut, Saskia Hilteman, Pratik Jagtap, Subina Mehta, etcFinished?
Mycobacterium tuberculosis NGS made easy: dataSeries of modules containing recorded videos by experts and tutorialsIllumina (wanting to expand to nanopore)Mapping & Variant calling, Molecular epidemiology of TB using NGS, Phylogenetics for studying TB evolution and epidemiologyDaniela Brites, Peter van Heusden, Galo A. Goig, Christoph StrittInitially funded trough TB projects of capacity building; currently no fundingReady to be used but also working on improvements


PartnersDescriptionPeople involved
Seq4AMRJPIAMR Network for Integrating Microbial Sequencing and Platforms for Antimicrobial ResistanceSaskia Hilteman
ELIXIR Emerging Microbiome CommunityBérénice 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!