Location: Egg and Poultry Production Safety Research Unit
Project Number: 6040-32000-012-002-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2021
End Date: May 30, 2026
Objective:
1. Cooperator will optimize pipeline and methods for analyzing metagenomic data.
2. Cooperator will evaluate reads2resistome using relevant data generated with the cooperator’s lab, in collaboration with the ARS PI, or directly provided by ARS PI.
Approach:
Reads2resistome is a publicly available pipeline on the ARS SCINet network that streamlines the analysis of bacterial genome sequences for antimicrobial resistance and virulence. The cooperator developed the tool through an Oak Ridge Institute for Science and Education (ORISE) agreement with ARS. The cooperator will continue to collaborate with ARS to identify the best way to optimize the pipeline for analyzing data generated via sequencing of the broiler chicken microbiome. ARS will provide relevant resources to generate data and/or directly provide data to evaluate the accuracy of reads2resistome and to utilize this software in analyses and research that will be published in peer-reviewed journals. Funds will provide support for research associates, students, equipment, supplies, travel, and cost of publications.
