ArticleNature communications2024
De novo diploid genome assembly using long noisy reads.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Review
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of young sex chromosomes.The Plant journal : for cell and molecular biology · 2026Article
- Article
- Article
- Haplotype-aware long-read error correction.Algorithms for molecular biology : AMB · 2026Article
- LORA: a polymorphic multi-sample long read assembly pipeline.NAR genomics and bioinformatics · 2026Article
- Strain, procedures, and tools for reproducible genetic transformation and genome editing of the emerging plant model Spirodela polyrhiza.The New phytologist · 2026Article
- Whole-genome sequencing reveals a possible molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro.PLoS genetics · 2026Article
- Evaluating genome assemblies with HMM-Flagger.bioRxiv : the preprint server for biology · 2026Article
- Article
- A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.G3 (Bethesda, Md.) · 2026Article
- FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.GigaScience · 2026Article
- Efficient near telomere-to-telomere assembly of Nanopore Simplex reads.bioRxiv : the preprint server for biology · 2025Article
- A closed-loop method for precise genome size estimation using HiFi reads.BMC genomics · 2025Article
- Diploid Genome Assembly of the Blastobotrys allociferrii Clinical Isolate CBS 18616.Mycopathologia · 2025Article
- A conserved terpene cyclase gene in Sanghuangporus for abscisic acid-related sesquiterpenoid biosynthesis.BMC genomics · 2025Article
- Unravelling the Chloroplast Genome of the Kazakh Apricot (Plants (Basel, Switzerland) · 2025Article
- xRead: a coverage-guided approach for scalable construction of read overlapping graph.GigaScience · 2025Article
- Beyond single references: pangenome graphs and the future of genomic medicine.Frontiers in genetics · 2025Review
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Authors and funding
8 authors.
Funding
Abstract
The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads.
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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.