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

Abstract

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 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. 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.

Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens

“…The first study ( 16 ) examined 92 strains from 76 patient and food samples by SNP calling and phylogenetic analysis. SNP calling was done by mapping sequencing reads to reference genomes using GalaxyTrakr's pipeline of the Center for Food Safety and Applied Nutrition (CFSAN) ( 18 ) and with NCBI Pathogen Detection, which uses genome assemblies and performs kmer-based clustering followed by 50-SNP single linkage clustering. Of the examined strains, 24 were from sporadic samples, and 16 were cultured from the same samples; hence, they were excluded from our reanalysis.…”

Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens

“…GalaxyTrakr is an instance of Galaxy 11 that was developed by the FDA as a bioinformatics platform for use by United States public health laboratories. However, it is particularly advantageous for educational use, as the computational tools included are only those typically used for studying microbial genomes in general, particularly those of pathogens (Gangiredla et al, 2021). After they assembled, annotated, and serotyped their isolate genomes, students were then asked to pursue specific questions and hypotheses related to genes and gene functional categories of interest in their isolates, including those relating to antibiotic resistance, virulence, phages, plasmids, transposons, etc.…”

“…Sequence data were processed according to the pipeline shown in Figure 1B. Bioinformatic processing and analyses were done in GalaxyTrakr (Gangiredla et al, 2021) or using the command line interface on a computer with an Ubuntu 16.04 LTS operating system. Short read data were quality checked using FastQC 4 version 0.72 or 0.69.…”

“…A bioinformatics workflow was developed and used for the QC, assembly, and annotation of Salmonella genomes (Figure 1B). This workflow was carried out primarily using GalaxyTrakr, an FDA Galaxy instance developed particularly for the use of public health laboratories for analyzing the genomes of foodborne pathogens (Gangiredla et al, 2021).…”

Research note: The resistome of commensal Escherichia coli isolated from broiler carcasses “produced without the use of antibiotics”a

“…Libraries were built using the Nextera XT DNA Library Preparation Kit (Illumina, Milan, Italy) and sequenced on Illumina MiSeq Platform which generates tagged 250 bp paired end reads. Unless otherwise indicated, all subsequent genomic analyses were performed on Galaxy Trakr platform ( Gangiredla et al, 2021 ). After performing a quality cleaning through TRIMMOMATIC, reads were de novo assembled using Shovill v.1.0.4, a standardized and fully automatic open-source pipeline for bacterial genome assembly.…”