6k citations · 6k across the 6 of their papers we have counts for
8 papers
Generating eukaryotic reference genome assemblies: Earth BioGenome Project quality standards and recommendations
Kerstin Howe, Dolores R. Agius, Tyler Alioto +45
Reference genome assemblies are foundational resources across the biological sciences as they begin to expose the fundamental building blocks of each species and the molecular tool…
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Haoyu Cheng, Mobin Asri, Julian Lucas +2
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 comput…
De novo reconstruction of satellite repeat units from sequence data
Yujie Zhang, Justin Chu, Haoyu Cheng +1
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble.…
Metagenome assembly of high-fidelity long reads with hifiasm-meta
Xiaowen Feng, Haoyu Cheng, Daniel Portik +1
Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome asse…
Robust haplotype-resolved assembly of diploid individuals without parental data
Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo +4
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction dat…
Haplotype-resolved de novo assembly with phased assembly graphs
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng +2
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into…
LVMapper: A Large-variance Clone Detector Using Sequencing Alignment Approach
Ming Wu, Pengcheng Wang, Kangqi Yin +3
To detect large-variance code clones (i.e. clones with relatively more differences) in large-scale code repositories is difficult because most current tools can only detect almost…
FMtree: A fast locating algorithm of FM-indexes for genomic data
Haoyu Cheng, Ming Wu, Yun Xu
Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text is widely accelerated by various compressed full-text indexes. These inde…