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Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience

View ORCID ProfileArnold Knijn, View ORCID ProfileValeria Michelacci, View ORCID ProfileMassimiliano Orsini, View ORCID ProfileStefano Morabito
doi: https://doi.org/10.1101/2020.05.14.095901
Arnold Knijn
1EURL for E. coli including VTEC, Istituto Superiore di Sanità, Dep. of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy
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Valeria Michelacci
1EURL for E. coli including VTEC, Istituto Superiore di Sanità, Dep. of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy
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Massimiliano Orsini
2Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
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Stefano Morabito
1EURL for E. coli including VTEC, Istituto Superiore di Sanità, Dep. of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy
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  • For correspondence: stefano.morabito@iss.it
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Abstract

Background: With the introduction of Next Generation Sequencing (NGS) and Whole-Genome Sequencing (WGS) in microbiology and molecular epidemiology, the development of an information system for the collection of genomic and epidemiological data and subsequent transparent and reproducible data analysis became indispensable. Further requirements for the system included accessibility and ease of use by bioinformatics as well as command line profane scientists.

Findings: The ARIES (Advanced Research Infrastructure for Experimentation in genomicS, https://aries.iss.it) platform has been implemented in 2015 as an instance of the Galaxy framework specific for use of WGS in molecular epidemiology. Here, the experience with ARIES is reported. Conclusions: During its five years existence, ARIES has grown into a well-established reality not only as a web service but as well as a workflow engine for the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. In fact, an environment has been created with the implementation of complex bioinformatic tools in an easy-to-use context allowing scientists to concentrate on what to do instead of how to do it.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://aries.iss.it

  • List of abbreviations

    AMR
    Antimicrobial Resistance
    API
    Application Programming Interface
    ARIES
    Advanced Research Infrastructure for Experimentation in genomicS
    CPU
    Central Processing Unit
    ECDC
    European Centre for Disease Prevention and Control
    EFSA
    European Food Safety Authority
    E. coli
    Escherichia coli
    EURL
    European Union Reference Laboratory
    GB
    GigaByte
    IRIDA
    Integrated Rapid Infectious Disease Analysis
    ISS
    Istituto Superiore di Sanità
    MLST
    MultiLocus Sequence Typing
    NAS
    Network Attached Storage
    NFS
    Network File System
    GS
    Next Generation Sequencing;
    NRL
    National Reference Laboratory
    PFGE
    Pulsed-field Gel Electrophoresis
    PHANtAsTiC
    Public Health Analysis of Nucleotides through Assembly, Typing and Clustering
    PT
    Pipeline Tool
    RAM
    Random Access Memory
    VTEC
    Verotoxigenic Escherichia coli
    WGS
    Whole Genome Sequencing
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    Posted May 16, 2020.
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    Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience
    Arnold Knijn, Valeria Michelacci, Massimiliano Orsini, Stefano Morabito
    bioRxiv 2020.05.14.095901; doi: https://doi.org/10.1101/2020.05.14.095901
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    Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience
    Arnold Knijn, Valeria Michelacci, Massimiliano Orsini, Stefano Morabito
    bioRxiv 2020.05.14.095901; doi: https://doi.org/10.1101/2020.05.14.095901

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