RT Journal Article
SR Electronic
T1 Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.14.095901
DO 10.1101/2020.05.14.095901
A1 Arnold Knijn
A1 Valeria Michelacci
A1 Massimiliano Orsini
A1 Stefano Morabito
YR 2020
UL http://biorxiv.org/content/early/2020/05/16/2020.05.14.095901.abstract
AB 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 StatementThe authors have declared no competing interest.AMRAntimicrobial ResistanceAPIApplication Programming InterfaceARIESAdvanced Research Infrastructure for Experimentation in genomicSCPUCentral Processing UnitECDCEuropean Centre for Disease Prevention and ControlEFSAEuropean Food Safety AuthorityE. coliEscherichia coliEURLEuropean Union Reference LaboratoryGBGigaByteIRIDAIntegrated Rapid Infectious Disease AnalysisISSIstituto Superiore di SanitàMLSTMultiLocus Sequence TypingNASNetwork Attached StorageNFSNetwork File SystemGSNext Generation Sequencing;NRLNational Reference LaboratoryPFGEPulsed-field Gel ElectrophoresisPHANtAsTiCPublic Health Analysis of Nucleotides through Assembly, Typing and ClusteringPTPipeline ToolRAMRandom Access MemoryVTECVerotoxigenic Escherichia coliWGSWhole Genome Sequencing