Yunxi Liu

Olivar automates variant-aware primer design for tiled amplicon sequencing of pathogens, improving mapping rates and coverage compared to existing methods.

This paper introduces Lemur and Magnet, lightweight tools for accurate taxonomic profiling of long-read metagenomic datasets, showing they run efficiently on laptops.

SeqScreen-Nano rapidly characterizes novel pathogens using ONT sequencing in resource-limited settings by identifying ORFs and classifying them functionally and taxonomically.

Variabel identifies low frequency intra-host variants from Oxford Nanopore sequencing data, outperforming existing tools for this task.

Squeegee identifies microbial contaminants in low biomass microbiomes using de novo analysis, showing high precision in simulated and real datasets.

This study analyzes over 7,000 SARS-CoV-2 datasets to reveal genomic diversity, showing iSNVs and small indels drive variation, and highlights implications for qRT-PCR and transmission tracking.