Florian P. Breitwieser

MMseqs2 taxonomy assigns taxonomic labels to metagenomic contigs using fragment extraction and weighted voting, achieving 2-18x speed improvements over existing tools.

KrakenHLL improves metagenomic classification by reducing false positives through unique k-mer coverage estimation, achieving better recall and F1-scores than existing methods.

The paper introduces AVARDA, a software package for analyzing VirScan data to deconvolute antiviral antibody responses, improving viral encephalitis diagnosis by 62.5% in a cohort.

Pavian is an R Shiny web application that visualizes and transforms Kraken and Centrifuge metagenomics classification outputs using interactive tables, heatmaps, flow diagrams, and a genome alignment viewer.