Florian Ingels

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.

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

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

The paper introduces a framework to efficiently enumerate k-mers from a collection of references based on metadata constraints, using a specialized data structure and demonstrating it on microbial and RNA-seq data.