Antoine Limasset

Chargé de Recherche CNRS, CRIStAL, Université de Lille
Member of the Bonsai Team

About Me

I am a CNRS researcher at the CRIStAL laboratory in Lille, France, where I am a member of the Bonsai bioinformatics team. My research focuses on developing efficient computational methods to analyze the massive amounts of data generated by DNA sequencing technologies, bridging the gap between theoretical computer science and practical biological data analysis. My goal is to create scalable, efficient, and accessible tools that enable new discoveries in genomics, transcriptomics, and metagenomics.

📚 Main Publications

2025

Fractional hitting sets for efficient multiset sketching
- Venue: Algorithms for Molecular Biology
- Tool: SuperSampler
K2R: Tinted de Bruijn Graphs implementation for efficient read extraction from sequencing datasets
- Venue: Bioinformatics Advances
- Tool: K2R
Hyper-k-mers: Efficient Streaming k-mers Representation
- Venue: International Conference on Research in Computational Molecular Biology (RECOMB)
- Tool: KFC
REINDEER2: practical abundance index at scale
- Venue: SPIRE2025
- Tool: Reindeer2
Accelerating k-mer-based sequence filtering
- Venue: bioRxiv (Preprint)
- - Tool: K2Rmini
OReO: optimizing read order for practical compression
- Venue: Bioinformatics Advances
- Tool: OREO

2024

Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors
- Venue: PeerJ
- Tool: MSALIMIT
Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets
- Venue: Bioinformatics (ISMB Proceedings)
- Tool: CBL
Brisk: Exact resource-efficient dictionary for k-mers
- Venue: bioRxiv (Preprint)
- Tool: Brisk

2023

Scalable sequence database search using partitioned aggregated Bloom comb trees
- Venue: Bioinformatics (ISMB Proceedings)
- Tool: PAC
Locality-preserving minimal perfect hashing of k-mers
- Venue: Bioinformatics (ISMB Proceedings)
- Tool: LPHASH

2020

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
- Venue: Bioinformatics
- Tool: BCOOL

2021

BLight: Efficient exact associative structure for k-mers
- Venue: Bioinformatics
- Tool: BLight
Toward optimal fingerprint indexing for large scale genomics
- Venue: *WABI
- Tool: NIQKI
Scalable long read self-correction and assembly polishing with multiple sequence alignment
- Venue: Scientific Reports
- Tool: CONSENT

2020

ELECTOR: evaluator for long reads correction methods
- Venue: NAR Genomics and Bioinformatics
- Tool: ELECTOR
A resource-frugal probabilistic dictionary and applications in bioinformatics
- Venue: Discrete Applied Mathematics
- Tool: SRC

2017

Fast and scalable minimal perfect hashing for massive key sets
- Venue: 16th International Symposium on Experimental Algorithms (SEA)
Novel approaches for the exploitation of high throughput sequencing data (PhD Thesis)
- Venue: Université Rennes 1

2016

Compacting de Bruijn graphs from sequencing data quickly and in low memory
- Venue: Bioinformatics (ISMB Proceedings)
Read mapping on de Bruijn graphs
- Venue: BMC Bioinformatics
- Tool: BGREAT

2014

On the representation of de Bruijn graphs
- Venue: International Conference on Research in Computational Molecular Biology (RECOMB)

📖 Other Publications

2022

Critical assessment of metagenome interpretation: the second round of challenges
- Venue: Nature Methods

2021

STRONG: metagenomics strain resolution on assembly graphs
- Venue: Genome Biology
- Tool: STRONG
Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga
- Venue: Science Advances

🛠️ Software Tools

All my projects are open-source. Here are some of the key software packages developed.

BCOOL: A conservative short-read error corrector using a meticulously cleaned de Bruijn graph.
BGREAT: A tool for mapping sequencing reads directly onto a de Bruijn graph.
BLIGHT: A static and exact k-mer dictionary using minimizer-partitioned MPHFs for high performance.
BRISK: An exact and dynamic dictionary for large k-mer sets, offering significant memory savings.
BRRR: A linear-time long-read correction tool based on the k-mer spectrum.
BWISE: A short-read assembler designed to handle highly heterozygous and polyploid genomes.
CBL: A dynamic k-mer set structure supporting fast set operations like union and intersection.
CONSENT: A scalable tool for long-read self-correction and assembly polishing.
ELECTOR: An evaluation tool for long-read error correction methods, providing detailed metrics.
K2R: An index that efficiently maps k-mers to the specific reads they came from (Tinted de Bruijn Graph).
KFC: A fast k-mer counter based on the novel and space-efficient hyper-k-mer data structure.
Kloe: A tool for compressing and retrieving k-mer sets from a specific dataset within a large collection.
LPHASH: A locality-preserving minimal perfect hash function library that is highly space-efficient for k-mer sets.
MSALIMIT: A benchmark framework for the systematic evaluation of Multiple Sequence Alignment techniques.
NIQKI: A tool for ultra-fast, large-scale comparison of genomic sketches using an inverted index.
ONIKA: An improved version of NIQKI with tunable fingerprints and a balanced inverted index.
OREO: A tool that reorders long reads based on a draft assembly to improve their compressibility.
OREOMINI: A lightweight version of OREO using one-bit MinHash sketches for fast read partitioning.
PAC: A scalable tool for indexing and querying k-mer presence in massive collections of sequencing data.
REINDEER2: An index for storing and querying k-mer abundances across large dataset collections.
STRONG: A pipeline for resolving microbial strains from metagenomic assembly graphs.
SUPERSAMPLER: A sketching tool that uses a fractional hitting set of super-k-mers for efficient comparison.

Team & Supervision

Current PhD Students

Yohan Hernandez-Courbevoie (PhD Director, 2024-present)
Timothé Rouzé (PhD Co-supervisor, 2023-present)
Léa Vandamme (PhD Director, 2021-present)

PhD Students

Coralie Rohmer (PhD Co-supervisor, 2019-2022)

Diploma

2025: “Habilitation à diriger des recherche” (post-doctoral degree authorizing the supervision of PhD students), Université de Lille
2017: Ph.D in Computer Science, Université de Rennes 1
- Thesis: Novel approaches for the exploitation of high throughput sequencing data
- Supervisors: Pierre Peterlongo and Dominique Lavenier
2014: M.Sc. in Computer Science, École Normale Supérieure de Rennes
2012: B.Sc. in Computer Science, École Normale Supérieure de Cachan

Professional Experience

2018 - Present: CNRS Researcher, CRIStAL, Lille, France
2017 -2018: Postdoctoral Researcher, Université Libre de Bruxelles, Belgium
- Worked on de novo assembly of heterozygous genomes.

Grants & Funding

2024: MIC INSERM (Principal Investigator), €554k
- Analyse efficace et évolutive du cancer par exploration transcriptomique avancée à grande échelle
2024: ANR (Member), €500k
- Shannon x Cray
2021: ANR JCJC (Principal Investigator), €227k
- Adequate graph structures for third-generation sequencing data exploration
2019: Region Haut de France PhD Grant (Principal Investigator), €150k

Professional Service

Conference Committees

Program Committee: RECOMB (2020-2024), ACM-BCB (2020-2024), ECCB/ISMB (2020-2024), SeqBim (2020-2024).
Organizational Committee: SPIRE (2021).

Reviewer Activities

Nature Methods, Nature Communication, Genome Research, Genome Biology, Nucleic Acids Research, Bioinformatics, Scientific Reports, and others.

Thesis Committees

Nastasija Mijovic (PhD Committee, 2023-2025)
Riku Walve (Examiner, 2022)
Svitlana Lukicheva (PhD Jury, 2021)
Théo Lemane (PhD Committee, 2020-2021)
Nadege Guiglielmoni (PhD Committee, 2019-2020)

Invited Talks & Presentations

2024: EMBL-EBI Kmer/sequence indexing workshop, Cambridge, UK
2024: Kmer days, Dijon, France
2023: ISMB, Lyon, France
2022: RECOMB, San Diego, US
2022: DSB, Düsseldorf, Germany
2022: TUDASTIC, Lille, France
2021: Kmer days, Marville, France
2019: Biata, Saint Petersburg, Russia
2018: RECOMB, Paris, France

Contact

Antoine Limasset CRIStAL (UMR 9189)
Université de Lille, Bâtiment ESPRIT
59655 Villeneuve d’Ascq, France

Email: antoine.limasset@cnrs.fr