Bio

I am a postdoctoral researcher at Pasteur Institute (Paris, France). My research work focuses on the development of scalable methods and software for processing metagenomics data.

I studied computer science at the university of Rennes. In 2014, I started my PhD under the supervision of Claire Lemaitre and Pierre Peterlongo working on large-scale de novo comparative metagenomics. I defended my PhD in 2017. In 2021, after three years as an independent game developer, I started a postdoc with Christopher Quince at Earlham Institute working on long-read metagenomics assembly. In 2024, I started a second postdoc with Rayan Chikhi at Pasteur Institute, working on an evolution of my long-read assembly methods for noisy Nanopore data.

Software

• MetaMDBG: fast and low-memory assembly for long metagenomics reads
• Simka: large-scale de novo comparative metagenomics based on efficient k-mer counting of multiple datasets
• SimkaMin: ultra-fast estimation of jaccard and bray-curtis distances using k-mer skecthes
• Leon: read compression based on probabilistic de-Bruijn graph
• Bloocoo: memory efficient read correction using a bloom filter

Publications

• High-quality metagenome assembly from simplex Nanopore reads with nanoMDBG. G Benoit, R James, S Raguideau, R Chikhi and C Quince; preprint, 2025
• High-quality metagenome assembly from long accurate reads with metaMDBG. G Benoit, S Raguideau, R James, A M Phillippy, R Chikhi and C Quince; Nature Biotechnology, 2024
• Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. DJ Richter, R Watteaux, T Vannier, J Leconte, P Frémont, G Reygondeau, N Maillet, N Henry, G Benoit, ..., O Jaillon; Elife, 2022
• SimkaMin: fast and resource frugal de novo comparative metagenomics. G Benoit, M Mariadassou, S Robin, S Schbath, P Peterlongo, C Lemaitre; Bioinformatics, 2020
• Multiple comparative metagenomics using multiset k-mer counting. G Benoit, P Peterlongo, M Mariadassou, E Drezen, S Schbath, D Lavenier, C Lemaitre; PeerJ Computer Science, 2016
• Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. G Benoit, C Lemaitre, D Lavenier, E Drezen, T Dayris, R Uricaru, G Rizk; BMC bioinformatics, 2015

Communications

Talks

• Seqbim, Rennes, 2024, Metagenome assembly from simplex Nanopore reads with NanoMDBG (chairman)
• Genome Informatics, Hinxton, 2024, Metagenome assembly from simplex Nanopore reads with NanoMDBG (chairman + evaluation committee)
• EBAME, Brest, 2024, Long-read metagenomics assembly (lecture + lab)
• EBAME, Brest, 2023, Long-read metagenomics assembly (lecture + lab)
• JOBIM, Lille, 2017, Simka: Large-scale de novo comparative metagenomics
• Seqbim, Orsay, 2015, Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph
• RCAM, Paris, 2015, Fast kmer-based method for estimating the similarity between numerous metagenomic datasets
• EBAME, Brest, 2015, Fast kmer-based method for estimating the similarity between numerous metagenomic datasets

Posters

• JOBIM, Clermont-Ferrand, 2015, Fast kmer-based method for estimating the similarity between numerous metagenomic datasets [best poster award]
• ECCB, Strasbourg, 2014, Bloocoo, a memory efficient read corrector

Other projects

• Eat'n eaten: an ecosystem sim game, developed in C# with Unity engine
• L'assemblage génomique ou "Résoudre le puzzle de la vie": a short film on genomic assembly that I made with Antoine Limmasset during our PhD (in french).