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A rapid and simple method for assessing and representing genome sequence relatedness

Abstract : C E N T R E M E R S E N N E Peer Community Journal is a member of the Centre Mersenne for Open Scientific Publishing http:// www.centre-mersenne.org/ Peer Community Journal Section: Genomics RESEARCH ARTICLE Published 2021-11-26 Cite as M Briand, M Bouzid, G Hunault, M Legeay, M Fischer-Le Saux and M Barret (2021) A rapid and simple method for assessing and representing genome sequence relatedness, Peer Community Journal, 1: e24. Correspondence martial.briand@inrae.fr Peer-review Peer reviewed and recommended by PCI Genomics, https://doi.org/10.24072/pci. genomics.100001 This article is licensed under the Creative Commons Attribution 4.0 License. A rapid and simple method for assessing and representing genome sequence relatedness M Briand1, M Bouzid1, G Hunault2, M Legeay3, M Fischer-Le Saux1, and M Barret1 Volume 1 (2021), article e24 https://doi.org/10.24072/pcjournal.37 Abstract Coherent genomic groups are frequently used as a proxy for bacterial species delineation through computation of overall genome relatedness indices (OGRI). Average nucleotide identity (ANI) is a widely employed method for estimating relatedness between genomic sequences. However, pairwise comparisons of genome sequences based on ANI is rela- tively computationally intensive and therefore precludes analyses of large datasets com- posed of thousands of genome sequences.In this work we proposed a workflow to com- pute and visualize relationships between genomic sequences. A dataset containing more than 3,500 Pseudomonas genome sequences was successfully classified with an alter- native OGRI based on k-mer counts in few hours with the same precision as ANI. A new visualization method based on zoomable circle packing was employed for assess- ing relationships among the 350 groups generated. Amendment of databases with these Pseudomonas groups greatly improved the classification of metagenomic read sets with k-mer-based classifier.
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Submitted on : Monday, February 7, 2022 - 5:49:55 PM
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Distributed under a Creative Commons Attribution 4.0 International License

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Martial Briand, M Bouzid, G Hunault, M Legeay, Marion Fischer-Le Saux, et al.. A rapid and simple method for assessing and representing genome sequence relatedness. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e24. ⟨10.24072/pcjournal.37⟩. ⟨hal-03560813⟩

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