In a new preprint, scientists from the National Human Genome Research Institute, the University of Washington, and other institutions describe HiCanu, a modified version of the Canu assembler designed specifically for PacBio HiFi reads. The team put the new assembler through its paces, reporting that it significantly outperformed traditional assembly methods — even getting through centromeres, segmental duplications, and other notoriously difficult regions. As lead authors Sergey Nurk (@sergeynurk) and Brian P. Walenz, corresponding authors Sergey Koren (@sergekoren) and Adam Phillippy (@aphillippy), and collaborators report, “HiFi is a major leap forward in terms of long-read read accuracy.” They add, “As…
UPDATE: The article is now published in the Annals of Human Genetics. A new preprint evaluates the utility of PacBio HiFi reads for assembly of a human genome. The study is a follow-up to a recent publication in Nature Biotechnology that introduced a technique to generate sequencing reads with both long read length and high accuracy. Evan Eichler discussed the challenges of segmental duplications during a presentation at SMRT Leiden in May. Illustration by Alex Cagan of the Sanger Institute. “Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads” comes from lead authors…
When scientists want to investigate human-specific evolution, the best place to start is often with a comparison to our closest cousins, the great apes. Some recent high-quality PacBio genome assemblies have provided solid new foundations for these projects, but gene annotation has proven challenging, particularly for segmental duplications — sets of gene families duplicated in the human lineage relative to our last common ancestor with the chimpanzee. Could these photocopied gene families be involved in human-specific traits like the development of a larger frontal cortex? Until now, technical limitations have stood in the way of answering that question. Two common…