دورية أكاديمية
أعرض في EDS

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

التفاصيل البيبلوغرافية
العنوان: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.
المؤلفون: Nurk S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA., Walenz BP; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA., Rhie A; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA., Vollger MR; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA., Logsdon GA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA., Grothe R; Pacific Biosciences, Menlo Park, California 94025, USA., Miga KH; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA., Eichler EE; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA., Phillippy AM; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA., Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA.
المصدر: Genome research [Genome Res] 2020 Sep; Vol. 30 (9), pp. 1291-1305. Date of Electronic Publication: 2020 Aug 14.
نوع المنشور: Evaluation Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, N.I.H., Intramural
اللغة: English
بيانات الدورية: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9518021 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-5469 (Electronic) Linking ISSN: 10889051 NLM ISO Abbreviation: Genome Res Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press, c1995-
مواضيع طبية MeSH: Genetic Variation*, High-Throughput Nucleotide Sequencing/*methods , Sequence Analysis, DNA/*methods, Alleles ; Animals ; Cell Line ; Chromosome Duplication ; DNA, Neoplasm ; DNA, Satellite ; Drosophila/genetics ; Genome, Human ; Haplotypes ; Humans ; Reproducibility of Results ; Software
مستخلص: Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced Pacific Biosciences (PacBio) HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultralong Oxford Nanopore Technologies (ONT) reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of nine complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance toward the complete assembly of human genomes.
(© 2020 Nurk et al.; Published by Cold Spring Harbor Laboratory Press.)
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معلومات مُعتمدة: F32 GM134558 United States GM NIGMS NIH HHS; R01 HG010169 United States HG NHGRI NIH HHS; R21 HG010548 United States HG NHGRI NIH HHS; U01 HG010971 United States HG NHGRI NIH HHS; R01 HG002385 United States HG NHGRI NIH HHS
المشرفين على المادة: 0 (DNA, Neoplasm)
0 (DNA, Satellite)
تواريخ الأحداث: Date Created: 20200818 Date Completed: 20211029 Latest Revision: 20240329
رمز التحديث: 20240329
مُعرف محوري في PubMed: PMC7545148
DOI: 10.1101/gr.263566.120
PMID: 32801147
قاعدة البيانات: MEDLINE
الوصف
تدمد:1549-5469
DOI:10.1101/gr.263566.120