Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph

1 code implementation • 6 Jun 2023 • Haoyu Cheng, Mobin Asri, Julian Lucas, Sergey Koren, Heng Li

Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational resources.

De novo reconstruction of satellite repeat units from sequence data

1 code implementation • 19 Apr 2023 • Yujie Zhang, Justin Chu, Haoyu Cheng, Heng Li

Existing algorithms for identifying satellite repeats either require the complete assembly of satellites or only work for simple repeat structures without HORs.

Metagenome assembly of high-fidelity long reads with hifiasm-meta

1 code implementation • 16 Oct 2021 • Xiaowen Feng, Haoyu Cheng, Daniel Portik, Heng Li

Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads.

Vocal Bursts Intensity Prediction

Robust haplotype-resolved assembly of diploid individuals without parental data

1 code implementation • 10 Sep 2021 • Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo, Klaus-Peter Koepfli, Lara Urban, Neil J. Gemmell, Heng Li

Routine single-sample haplotype-resolved assembly remains an unresolved problem.

Haplotype-resolved de novo assembly with phased assembly graphs

no code implementations • 3 Aug 2020 • Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome.

Genomics Quantitative Methods