HudsonAlpha Institute for Biotechnology

Khufu is a genomics analysis platform offered by HudsonAlpha Institute for Biotechnology, supporting breeding and research programs through low-coverage whole-genome sequencing. Unlike fixed-marker arrays, Khufu can identify established and previously unknown genetic markers, helping researchers investigate variation across an entire genome at a fraction of standard costs. Its services combine high-throughput DNA extraction, 96-well plate library preparation, and sequencing with customizable analysis options.

Khufu Core maps short-read sequencing data to a reference genome to generate genome-wide SNP calls, with imputation and options for array-based or parent-guided genotyping. Khufu Trait Discovery adds phenotype data to identify genetic markers or haplotype regions associated with traits such as disease, drought, or pest resistance, as well as size and coloring. For programs seeking broader variation, KhufuPAN uses founder data to build a custom pangenome graph that can increase callable markers and include structural variants. Deliverables vary by service and may include genotype or panmap files, statistical results, and visual reports.