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microGalaxy logo{:.sc-intro-left}

Welcome to microGalaxy!

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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!


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Join the μGalaxy Community

Anybody interested in microbiology in Galaxy is welcome to join our microGalaxy interest group! Everybody is Welcome!

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.

Galaxy Training Network Tutorials tagged with #microGalaxy

<iframe src="https://training.galaxyproject.org/training-material/tags/microgalaxy/embed.html" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>

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

<iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?query=microgalaxy" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>

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:

<iframe id="inlineFrameExample" title="Microbial related tools" width="100%" height="600" frameBorder="0" src="https://galaxyproject.github.io/galaxy_tool_metadata_extractor/microgalaxy/"> </iframe>

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
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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
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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
{:width="100px"} JPIAMR: Global Coordination of Antimicrobial Resistance Research Website
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