microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data

Nasr, E.; Amato, P.; Bhardwaj, A.; Blankenberg, D.; Brites, D.; Cumbo, F.; Do, K.; Ferrari, E.; Griffin, T. J.; Gruening, B.; Hiltemann, S.; Jagtap, P.; Mehta, S.; Metris, K. L.; Momin, S.; Oba, A.; Pavloudi, C.; Pechlivanis, N.; Peguilhan, R.; Psomopoulos, F.; Rosic, N.; Schatz, M. C.; Schiml, V. C.; Siguret, C.; Soranzo, N.; Stubbs, A.; Van Heusden, P.; Vohra, M.; microGalaxy Community,; Zierep, P.; Batut, B.

doi:10.1101/2024.12.23.629682

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bioRxiv · 10.1101/2024.12.23.629682

microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data

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Abstract

The explosion of microbial omics data has outpaced the ability of many researchers to analyze it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab: a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platforms utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbial science. The Microbiology Galaxy Lab enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org, microbiology.usegalaxy.eu, microbiology.usegalaxy.org.au, microbiology.usegalaxy.fr).

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Nasr, E., Amato, P., Bhardwaj, A., Blankenberg, D., Brites, D., Cumbo, F., Do, K., Ferrari, E., Griffin, T. J., Gruening, B., Hiltemann, S., Jagtap, P., Mehta, S., Metris, K. L., Momin, S., Oba, A., Pavloudi, C., Pechlivanis, N., Peguilhan, R., Psomopoulos, F., Rosic, N., Schatz, M. C., Schiml, V. C., Siguret, C., Soranzo, N., Stubbs, A., Van Heusden, P., Vohra, M., microGalaxy Community,, Zierep, P., Batut, B.. 2024-12-27. microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data. https://doi.org/10.1101/2024.12.23.629682

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