Antoine Limasset

Toward space-optimal approximate colored indexes at scale

This paper introduces Zindex, a space-efficient indexing framework for large-scale sequence repositories, achieving compact storage and fast query performance with novel interleaved filters and merging mechanisms.

Minimizer Density revisited: Models and Multiminimizers

This paper revisits the concept of density in k-mer-based sequence analysis, introduces multiminimizers as a novel technique, and proposes deduplicated density as a new metric.

Super Bloom: Fast and precise filter for streaming k-mer queries

The paper introduces Super Bloom, a Bloom filter variant for streaming k-mer queries, which improves cache efficiency and reduces false positives.

Accelerating k-mer-based sequence filtering

The paper introduces K2Rmini, a tool that efficiently filters sequences based on k-mer matches, achieving 2 Gbp/s on a consumer laptop.

Inverted colored de Bruijn Graph for practical kmer sets storage

The paper introduces kloe, a compression method for k-mer multi-sets that enables targeted decompression of specific samples' k-mer content.

Compressed inverted indexes for scalable sequence similarity

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

REINDEER2: practical abundance index at scale

REINDEER2 provides a scalable, dynamic abundance index for RNA datasets, achieving faster construction and accurate abundance recovery.

K2R: Tinted de Bruijn Graphs implementation for efficient read extraction from sequencing datasets

K2R efficiently indexes sequencing datasets to identify reads containing specific k-mers, outperforming existing methods in speed and resource usage.

Brisk: Exact resource-efficient dictionary for k-mers

This paper introduces Brisk, a resource-efficient k-mer dictionary that reduces memory usage and improves throughput compared to existing methods.

Hyper-k-mers: efficient streaming k-mers representation

The paper introduces hyper-k-mers, a more efficient k-mer representation, and presents KFC, a tool that significantly reduces memory usage and improves speed for k-mer counting.

Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors

The paper evaluates multiple sequence alignment methods for third-generation sequencing errors using an automated pipeline and finds that performance varies with sequencing depth, genome characteristics, and error patterns.

Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets

The paper introduces CBL, a dynamic and exact k-mer set representation that outperforms existing methods and supports in-place set operations.

Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching

This paper introduces a new sketching method for genomic data that reduces space and memory usage while maintaining efficiency and accuracy compared to existing tools.

Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees

The paper introduces PAC, a scalable approximate membership query data structure for large sequence collections, achieving faster construction and query times than existing methods.

Critical Assessment of Metagenome Interpretation - the second round of challenges

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Toward optimal fingerprint indexing for large scale genomics

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

BLight: Efficient exact associative structure for k-mers

BLight is a memory-efficient data structure for associating unique identifiers with k-mers and querying them at high speed.

CONSENT: Scalable long read self-correction and assembly polishing with multiple sequence alignment

CONSENT corrects long reads using multiple sequence alignment and de Bruijn graphs, outperforming existing methods on Oxford Nanopore data and enabling efficient processing of ultra-long reads.

Metagenomics Strain Resolution on Assembly Graphs

STRONG identifies strains de novo from metagenome samples using coassembly, binning, and a Bayesian algorithm to resolve haplotypes and abundances.

ELECTOR: Evaluator for long reads correction methods

ELECTOR evaluates long reads correction methods by providing efficient and comprehensive metrics to assess quality improvements.

Read correction for non-uniform coverages

This paper introduces BCT, a tool that improves read correction for non-uniform coverage data by cleaning De Bruijn graphs and local alignment, preserving rare variants and improving accuracy in RNA-seq and metagenomic datasets.

Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs

The paper introduces Bcool, a short-read correction method using compacted de Bruijn graphs, achieving higher accuracy and scalability than existing k-mer-based approaches.