Rare diseases affect 30 million people in the USA and more than 300–400 million
worldwide, often causing chronic illness, disability, and premature death. Traditional …

Publication of the complete genome sequence of Arabidopsis thaliana, the first plant
reference genome, in December 2000 heralded the beginning of the plant genome era …

Missing heritability in genome-wide association studies defines a major problem in genetic
analyses of complex biological traits,. The solution to this problem is to identify all causal …

INTRODUCTION Modern genomics depends on inexpensive short-read sequencing.
Sequenced reads up to a few hundred base pairs in length are computationally mapped to …

Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to
crop evolution, domestication, and improvement. Here, we assembled 31 high-quality …

Typical genotyping workflows map reads to a reference genome before identifying genetic
variants. Generating such alignments introduces reference biases and comes with …

Soybean is one of the most important vegetable oil and protein feed crops. To capture the
entire genomic diversity, it is needed to construct a complete high-quality pan-genome from …

Long-read sequencing technologies have now reached a level of accuracy and yield that
allows their application to variant detection at a scale of tens to thousands of samples …

The human reference genome represents only a small number of individuals, which limits its
usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for …

Genetic variant calling from DNA sequencing has enabled understanding of germline
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …