David L. Dill

Aquila uses linked-read data to assemble diploid genomes and detect genetic variants, achieving high coverage and accurate phasing of SNPs, indels, and structural variants.

Aquila_stLFR is a tool for diploid genome assembly and structural variant calling using stLFR linked-read data, achieving high sensitivity for deletions and specificity for insertions.

The paper applies haplotype-based computational genetic mapping to large-scale mouse phenotypic datasets to identify genetic factors affecting biomedical traits.