Over the past decade, long-read, single-molecule DNA sequencing technologies have
emerged as powerful players in genomics. With the ability to generate reads tens to …

Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme
phenotypes to conduct economical and rapidly linked marker screening or quantitative trait …

We present YaHS, a user-friendly command-line tool for the construction of chromosome-
scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal …

Abstract The Telomere-to-Telomere consortium recently assembled the first truly complete
sequence of a human genome. To resolve the most complex repeats, this project relied on …

Advancing crop genomics requires efficient genetic systems enabled by high-quality
personalized genome assemblies. Here, we introduce RagTag, a toolset for automating …

November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which
aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant …

High-quality and complete reference genome assemblies are fundamental for the
application of genomics to biology, disease, and biodiversity conservation. However, such …

The current human reference genome, GRCh38, represents over 20 years of effort to
generate a high-quality assembly, which has benefitted society,. However, it still has many …

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages
the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies …

Abstract High-order three-dimensional (3D) interactions between more than two genomic
loci are common in human chromatin, but their role in gene regulation is unclear. Previous …