GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians
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Gangiredla, Jayanthi
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GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians
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Background: Processing 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 userfriendliness
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.
Results: In 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.
Conclusions: GalaxyTrakr 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.
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Center for Food Safety and Applied Nutrition at the U.S. Food and Drug Administration
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BMC Genomics (2021) 22:114
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