ArticleGenome research2017
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 227 papers.
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Who cites it
227 citing papers in PubMed.
- A phase II single-arm study of pembrolizumab with enzalutamide in men with metastatic castration-resistant prostate cancer progressing on enzalutamide alone.Journal for immunotherapy of cancer · 2020Trial
- Haplotype-resolved genome of a dry-preservable cell line reveals chromosome evolution and DNA damage.Life science alliance · 2026Article
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
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- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing.bioRxiv : the preprint server for biology · 2026Article
- Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.Life (Basel, Switzerland) · 2026Article
- Accelerated long-read variant calling with Clair3 for whole-genome sequencing.Bioinformatics (Oxford, England) · 2026Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states.Nature communications · 2026Article
- Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes.Cell systems · 2026Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- Within-host diversity and phased variant analysis reveal structures and recombination of Helicobacter pylori subpopulations in stomach.GigaScience · 2026Article
- The Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation.Nature communications · 2026Article
- Article
- Gene duplication, horizontal gene transfer, and trait trade-offs drive evolution of postfire resource acquisition in pyrophilous fungi.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass.Nature communications · 2025Article
- Graph-based deep reinforcement learning for haplotype assembly with Ralphi.Genome research · 2025Article
- Long-read reconstruction of many diverse haplotypes with devider.Genome research · 2025Article
167 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Many tools have been developed for haplotype assembly-the reconstruction of individual haplotypes using reads mapped to a reference genome sequence. Due to increasing interest in obtaining haplotype-resolved human genomes, a range of new sequencing protocols and technologies have been developed to enable the reconstruction of whole-genome haplotypes. However, existing computational methods designed to handle specific technologies do not scale well on data from different protocols. We describe a new algorithm, HapCUT2, that extends our previous method (HapCUT) to handle multiple sequencing technologies. Using simulations and whole-genome sequencing (WGS) data from multiple different data types-dilution pool sequencing, linked-read sequencing, single molecule real-time (SMRT) sequencing, and proximity ligation (Hi-C) sequencing-we show that HapCUT2 rapidly assembles haplotypes with best-in-class accuracy for all data types. In particular, HapCUT2 scales well for high sequencing coverage and rapidly assembled haplotypes for two long-read WGS data sets on which other methods struggled. Further, HapCUT2 directly models Hi-C specific error modalities, resulting in significant improvements in error rates compared to HapCUT, the only other method that could assemble haplotypes from Hi-C data. Using HapCUT2, haplotype assembly from a 90× coverage whole-genome Hi-C data set yielded high-resolution haplotypes (78.6% of variants phased in a single block) with high pairwise phasing accuracy (∼98% across chromosomes). Our results demonstrate that HapCUT2 is a robust tool for haplotype assembly applicable to data from diverse sequencing technologies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.