Yoann Dufresne

The paper introduces a method to perform set operations on k-mers using compacted representations, achieving efficient memory usage and high throughput.

Kaminari improves approximate k-mer query performance by using k-mer minimizers and integer compression, outperforming Bloom filters in memory and speed with minimal false positive impact.

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

The paper introduces the Backpack Quotient Filter (BQF), a data structure for querying k-mer abundance with improved space efficiency compared to the Counting Quotient Filter.

BioConvert simplifies life science data format conversion by aggregating tools and providing a unified interface, supporting 50 formats and 100 conversions.

This work constructs the largest human pangenome graphs by integrating 52 haplotypes and two synthetic references, comparing five tools to evaluate their representation of genetic variation.

The paper introduces a new compression tool for colored de Bruijn graphs, achieving better compression than existing tools across various datasets.

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.

MATAM improves taxonomic assignment in metagenomics by accurately assembling short reads into marker genes, outperforming existing methods in error rates and genome recovery.