Author

Clément Agret

Centre National de la Recherche ScientifiqueORCID 0000-0002-7404-7253Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 3 Organism:bacteria (other)· 2 Research Focus:benchmarking· 2 Research Focus:database / resource· 2 Approach:statistical model· 2 Approach:experimental assay· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Antoine LimassetiD· 2 shared Bastien CazauxiD· 2 shared Alban MancheroniD· 1 shared Annie ChâteauiD· 1 shared Florian IngelsiD· 1 shared Gaëtan DrociD· 1 shared Gautier SarahiD· 1 shared Léa VandammeiD· 1 shared

Activity by Year

2021-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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2 shared papersBioinformatics

Antoine LimassetORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

Compressed inverted indexes for scalable sequence similarity

Florian Ingels, Léa Vandamme, Mathilde Girard, Clément Agret, Bastien Cazaux, Antoine Limasset

The paper introduces Onika, a system using inverted indexes for efficient sequence similarity search, improving scalability and performance over existing tools.

bioRxiv · Nov 21, 2025 · PreprintBioinformatics

RedOak: a reference-free and alignment-freestructure for indexing a collection of similargenomes

Clément Agret, Annie Château, Gaëtan Droc, Gautier Sarah, Manuel Ruíz, Alban Mancheron

RedOak indexes and compresses large collections of similar genomes without a reference or alignment, enabling efficient sequence queries.

The Journal of Open Source Software · Dec 28, 2022Peer-reviewedBioinformatics

Toward optimal fingerprint indexing for large scale genomics

Clément Agret, Bastien Cazaux, Antoine Limasset

The paper introduces NIQKI, a novel indexing method for genomic databases that improves query speed and scalability compared to existing approaches.

bioRxiv · Nov 4, 2021 · PreprintBioinformatics