دورية أكاديمية
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HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.

التفاصيل البيبلوغرافية
العنوان: HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.
المؤلفون: Holt JM; Computational Biology, PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, United States., Saunders CT; Computational Biology, PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, United States., Rowell WJ; Computational Biology, PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, United States., Kronenberg Z; Computational Biology, PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, United States., Wenger AM; Computational Biology, PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, United States., Eberle M; Computational Biology, PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, United States.
المصدر: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Feb 01; Vol. 40 (2).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Oxford : Oxford University Press, c1998-
مواضيع طبية MeSH: High-Throughput Nucleotide Sequencing* , Genome, Human*, Humans ; Sequence Analysis, DNA ; Algorithms ; Haplotypes ; Tandem Repeat Sequences
مستخلص: Motivation: In diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased.
Results: We developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation.
Availability and Implementation: HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https://github.com/PacificBiosciences/HiPhase.
(© The Author(s) 2024. Published by Oxford University Press.)
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تواريخ الأحداث: Date Created: 20240125 Date Completed: 20240209 Latest Revision: 20240228
رمز التحديث: 20240229
مُعرف محوري في PubMed: PMC10868326
DOI: 10.1093/bioinformatics/btae042
PMID: 38269623
قاعدة البيانات: MEDLINE
الوصف
تدمد:1367-4811
DOI:10.1093/bioinformatics/btae042