Lore Depuydt

Extracting and Updating Compact Colored k-mer Indexes

This paper introduces efficient methods to update colored k-mer indexes without rebuilding them from scratch, enabling dynamic maintenance of large genomic collections.

Fast Set Operations for Compact k-mer Sets

The paper introduces efficient set operations for SBWT-encoded k-mer spectra, enabling memory-efficient processing of large genomic datasets.

Columba: Fast Approximate Pattern Matching withOptimized Search Schemes

Columba is a high-performance lossless aligner for Illumina sequencing data that outperforms existing tools in speed and memory efficiency, particularly for large datasets.

Run-length compressed metagenomic read classification with SMEM-finding and tagging

This paper introduces a run-length compressed metagenomic read classification method that outperforms existing tools in accuracy and runtime while maintaining efficient memory usage.

b-move: faster bidirectional character extensions in a run-length compressed index

The paper introduces b-move, a bidirectional extension of the move structure for run-length compressed indices, achieving faster character extensions than existing methods while maintaining memory efficiency.