SNiPgenie: A tool for microbial SNP site detection from whole genome sequencing data

Review Tool reports UNDERSTANDING AND CONTEXTUALIZING THE REPORTS Readers of these automated manuscript Review Tool reports are encouraged to use them to support them in performing their own assessment and ‘health check’ on a preprint prior to it completing peer review. However, these should only be used as a guide, read within the overall context of the article itself, and should never replace full peer review. Please ensure you read the article fully alongside these and familiarize yourself with the tools and how they work, using the links provided below. These reports are published under the terms of the Creative Commons Attribution License ITHENTICATE® REPORT iThenticate® (https://www.ithenticate.com) checks the submitted article against an extensive database of articles from the internet and scholarly publications and highlights where similar sentences or phrases have been used previously, including in the author’s own published work. Each individual match is given a percentage score based on how much it overlaps with the previously existing work, and an overall similarity score is given. The report generated from this are included here for transparency and can be cited independently using the DOI below. • FAQs: https://www.ithenticate.com/products/faqs • Help pages: https://help.turnitin.com/ithenticate/ithenticate-user/ithenticate-user.htm#TheSimilarityReport How to cite the iThenticate report for this article: Farrell D, Perets V , Gordon SV. iThenticate report for: SNiPgenie: A tool for microbial SNP site detection from whole genome sequencing data. Access Microbiology. 2025. https://doi.org/10.1099/acmi.0.001021.v1.1 ACMI-S-25-00100.pdf By Damien Farrell WORD COUNT 2660 TIME SUBMITTED18-MAR-2025 08:19PM PAPER ID 115227647 3 2 3 5 8 9 12 13 1 3 3 4 5 6 7 1 1 1 1 11 1 1 1 1 1 1 1 4 24% SIMILARITY INDEX 1 2 3 4 5 6 7 8 ACMI-S-25-00100.pdf ORIGINALITY REPORT PRIMARY SOURCES github.com Internet Damien Farrell, Joseph Crispell, Stephen V. Gordon. " Updated functional annotation of the AF2122/97 reference genome ", Cold Spring Harbor Laboratory, 2019 Crossref Posted Content dmnfarrell.github.io Internet www.frontiersin.org Internet www.ncbi.nlm.nih.gov Internet pure.uva.nl Internet Balamurugan Jagadeesan, Peter Gerner-Smidt, Marc W. Allard, Sébastien Leuillet et al. "The use of next generation sequencing for improving food safety: Translation into practice", Food Microbiology, 2019 Crossref Catriona P. Harkins, Kerry A. Pettigrew, Katarina Oravcová, June Gardner et al. "The micro-evolution 330 words — 15% 50 words — 2% 45 words — 2% 25 words — 1% 14 words — 1% 11 words — 1% 9 words — < 1% 9 words — < 1% 9 10 11 12 13 EXCLUDE QUOTESOFF EXCLUDE BIBLIOGRAPHYON EXCLUDE SOURCESOFF EXCLUDE MATCHESOFF and epidemiology of Staphylococcus aureus colonization during atopic eczema disease flare", Journal of Investigative Dermatology, 2017 Crossref Kilian J. Murphy, Andrew W. Byrne, Nicola Marples, Maria J.H. O’Hagan et al. "Wildlife response to land- use change forces encounters between zoonotic disease hosts and farms in agricultural landscapes", Agriculture, Ecosystems & Environment, 2025 Crossref Melese Yilma Zaba, Sebsib Neway, Damien Farrell, Eva Denion et al. "Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia", Microbiology Society, 2024 Crossref Posted Content www.microbiologyresearch.org Internet Jennie Pryce. "Advances in breeding of dairy cattle", Burleigh Dodds Science Publishing, 2019 Publications hdl.handle.net Internet 8 words — < 1% 8 words — < 1% 8 words — < 1% 6 words — < 1% 6 words — < 1%