Michael Alonge

TL;DR: The optimization of circular consensus sequencing (CCS) is reported to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb).

TL;DR: This work presents RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes and demonstrates the scalability and utility of the tool.

TL;DR: This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions, and showed how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production.

TL;DR: RaGOO is presented, an open-source reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in just minutes and outperforms error-prone reference-free methods and enable rapid pan-genome analysis.

TL;DR: This paper used long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres, which consist of megabase-scale tandemly repeated satellite arrays, which support CENTROMERE SPECIFIC HISTONE H3 occupancy and are densely DNA methylated.