Efficient telomere-to-telomere genome assembly with nanopore reads using hifiasm | LC 25

Biography

Haoyu Cheng is an Assistant Professor at the Department of Biomedical Informatics and Data Science (BIDS) at Yale University. His research is dedicated to creating highly efficient computational methodologies for genomic applications such as genome assembly, read alignment, variant calling, and string indexing. He has developed a series of de novo genome assembly algorithms (e.g. hifiasm) that have been extensively utilized across a variety of large-scale sequencing projects.

Abstract

High-quality telomere-to-telomere (T2T) assembly is the ultimate goal of de novo genome assembly. Existing T2T assembly algorithms achieve this by integrating multiple types of long-read data, a process that is not only costly but also requires a substantial DNA input, making it impractical for many clinical and large-scale studies. Here, we introduce hifiasm (ONT), an ultra-fast algorithm designed to directly correct and assemble Oxford Nanopore Technologies simplex reads. Our results show that hifiasm (ONT) is an order of magnitude faster than existing pipelines while eliminating the need for high-performance GPUs. Most importantly, we demonstrate that hifiasm (ONT) enables T2T assembly using only non-ultra-long, standard Oxford Nanopore Technologies simplex reads, which are significantly more cost-efficient and easier to obtain. These improvements greatly expand the applicability of T2T assembly to real-world clinical settings and large-scale genomic studies.