Daniel N. Baker

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

Dashing 2 improves genomic sketching by incorporating k-mer multiplicities and scaling all-pairs comparisons to millions of sequences using locality-sensitive hashing.

The paper introduces H+, a scale-agnostic and group-balance invariant discordance metric for clustering, and provides scalable methods to compute it.

minicore provides fast and memory-efficient scRNA-seq clustering using various distance measures, achieving results on large datasets in minutes with minimal resources.

Megadepth efficiently quantifies coverage in BigWig and BAM files, outperforming existing tools in speed and memory usage.

Dashing estimates genomic similarities quickly and accurately using HyperLogLog, outperforming MinHash-based methods for large datasets.

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