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. 2022 Mar 26;23:235. doi: 10.1186/s12864-022-08437-4

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — Box-plots representing the impact of downsampled paired-end reads (i.e. 2x150bp) of Listeria monocytogenes on misidentified alleles against reference at extended (A) or restricted (B) scales, according to reference genomes (i.e. ATCC19114, ATCC19115 and ATCCBAA679) and cgMLST workflows including BIGSdb (n = 420), INNUENDO (n = 336), GENPAT (n = 420), SeqSphere (n = 420), BioNumerics (n = 420) and MentaLiST (n = 420). The targeted read depth (Dr: 10X, 20X, 30X, 40X, 50X, 60X, 70X, 80X, 90X and 100X) were prepared according to kmer depth (Dk): 8X, 15X, 23X, 30X, 38X, 45X, 52X, 60X, 67X, 75X) setting of BBNorm (read length R = 150 and kmer size K = 30). Because of internal firewall, the INNUca assembler integrated into the cgMLST workflow INNUENDO cannot not perform assemblies of paired-end reads with read depth of coverage of 20X (n = 42) and 10X (n = 42)