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. 2023 Dec 14;14:1225207. doi: 10.3389/fmicb.2023.1225207

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Copyright © 2023 Lindsey, Gladney, Huang, Griswold, Katz, Dinsmore, Im, Kucerova, Smith, Lane and Carleton.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Downsampling for limits of detection. Representative species of Campylobacter, Escherichia, Listeria, Salmonella, and Vibrio were downsampled from 50× to 0.5× and analyzed with the ANIm algorithm. Genome coverage is plotted on the x-axis; the natural log of N50 (lnN50) is plotted on the left y-axis; and percent change from ANI at 50× is plotted on the right y-axis. The dotted blue line shows the average N50 for all the assemblies. The dark green line indicates the aggregate ANI values, or the average percentage that each ANI value deviated from what it was at 50×. Coverage cutoff of 10× was established based on this analysis, as species identification is not reliable below 10×. Additionally, the aggregate ANI begins accruing below 10×, gaining larger standard deviations.