Representation counts: the impact of embedding models on disease detection tasks from microbiome sequencing data

Benchmarking of viral quasispecies assembly algorithms

The impact of sequencing errors and contaminating viruses on SARS-CoV-2 variant detection by sequencing wastewater-sourced viral RNA

SARS-CoV-2 lineage abundance quantification in wastewater: a benchmark study for the identification of optimal reference set design

Effect of Output Granularity on SARS-CoV-2 Variant Abundance Estimates using Domestic Wastewater Sequencing

Kallisto Repurposed: Using sequencing reads from the spike, nucleocapsid, and a middle region of nsp3 in the kallisto pipeline to better predict SARS-CoV-2 variants in wastewater