PCI Genomics

Title *

A rapid and simple method for assessing and representing genome sequence relatednessuse asterix (*) to get italics

Authors *

M Briand, M Bouzid, G Hunault, M Legeay, M Fischer-Le Saux, M BarretPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2020

Picture *

Abstract *

<p>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 relatively computationally intensive and therefore precludes analyses of large datasets composed of thousands of genome sequences. In this work we proposed a workflow to compute and visualize relationships between genomic sequences. A dataset containing more than 3,500 *Pseudomonas* genome sequences was successfully classified with an alternative 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 assessing 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. The developed workflow was integrated in the user-friendly KI-S tool that is available at the following address: https://iris.angers.inra.fr/galaxypub-cfbp.</p>

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https://www.ncbi.nlm.nih.gov/genome/You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

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https://sourcesup.renater.fr/wiki/ki-s/You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@genomics.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint. *

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Keywords (optional)

ANI, k -mers, genome sequence relatedness, similarity matrix representation, circle packing, Pseudomonas , metagenome

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Bioinformatics, Metagenomics

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Submission date

2019-11-07 16:37:56

Recommender

B. Jesse Shapiro

Reviewers

Gavin Douglas

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