GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians

BMC Genomics

Melanie Prarat¹  Jayanthi Gangiredla²  Thomas Farrell³  Charles Strittmatter³  Justin Payne³  Hugh Rand³  James B. Herrick⁴  Errol Strain⁵  Daniel Benisatto⁶  Kevin Libuit⁷  Magaly Toro⁸  Jimmy Sanders⁹  William J. Wolfgang^1,10 

[1] Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, 43068, Reynoldsburg, Ohio, USA;Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 20708, Laurel, MD, USA;Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 20740, College Park, MD, USA;Center for Genome and Metagenome Studies, James Madison University, 22807, Harrisonburg, VA, USA;Center for Veterinary Medicine, U.S. Food and Drug Administration, 20708, Laurel, MD, USA;DRT Strategies, 22203, Arlington, VA, USA;Division of Consolidated Laboratory Services, Department of General Services, 23219, Richmond, VA, USA;Libuit Scientific LLC, 23219, Richmond, VA, USA;Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile;SDS Solutions, Inc, 22152, Springfield, VA, USA;Wadsworth Center, New York State Department of Health, 12201, Albany, NY, USA;

关键词: Galaxy;    Biosurveillance;    Whole genome sequencing;    Food safety;    Public health;    GenomeTrakr;    Genomic surveillance;   

DOI  :  10.1186/s12864-021-07405-8

来源: Springer

【 摘 要 】

BackgroundProcessing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstacles for smaller laboratories, or laboratories not affiliated with larger projects, which may not have dedicated bioinformatics staff or computing power to effectively use genomic data to protect public health. Building on the success of the cloud-based Galaxy bioinformatics platform (http://galaxyproject.org), already known for its user-friendliness and powerful WGS analytical tools, the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration (FDA) created a customized ‘instance’ of the Galaxy environment, called GalaxyTrakr (https://www.galaxytrakr.org), for use by laboratory scientists performing food-safety regulatory research. The goal was to enable laboratories outside of the FDA internal network to (1) perform quality assessments of sequence data, (2) identify links between clinical isolates and positive food/environmental samples, including those at the National Center for Biotechnology Information sequence read archive (https://www.ncbi.nlm.nih.gov/sra/), and (3) explore new methodologies such as metagenomics. GalaxyTrakr hosts a variety of free and adaptable tools and provides the data storage and computing power to run the tools. These tools support coordinated analytic methods and consistent interpretation of results across laboratories. Users can create and share tools for their specific needs and use sequence data generated locally and elsewhere.ResultsIn its first full year (2018), GalaxyTrakr processed over 85,000 jobs and went from 25 to 250 users, representing 53 different public and state health laboratories, academic institutions, international health laboratories, and federal organizations. By mid-2020, it has grown to 600 registered users and processed over 450,000 analytical jobs. To illustrate how laboratories are making use of this resource, we describe how six institutions use GalaxyTrakr to quickly analyze and review their data. Instructions for participating in GalaxyTrakr are provided.ConclusionsGalaxyTrakr advances food safety by providing reliable and harmonized WGS analyses for public health laboratories and promoting collaboration across laboratories with differing resources. Anticipated enhancements to this resource will include workflows for additional foodborne pathogens, viruses, and parasites, as well as new tools and services.

【 授权许可】

CC BY