Article Dans Une Revue Peer Community Journal Année : 2021

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

Résumé

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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hal-03560813 , version 1 (19-02-2025)

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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, 2021, 1, pp.e24. ⟨10.24072/pcjournal.37⟩. ⟨hal-03560813⟩
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