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Relevant bibliographies by topics / PacBio HiFi sequencing

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Journal articles

Academic literature on the topic 'PacBio HiFi sequencing'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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Journal articles on the topic "PacBio HiFi sequencing"

1

Han, Yanhua, Jinling He, Minghui Li, et al. "Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology." Microorganisms 12, no. 12 (2024): 2482. https://doi.org/10.3390/microorganisms12122482.

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Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio’s high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, su

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2

Zhang, Tong, Weiqing Xing, Aoming Wang, et al. "Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes." International Journal of Molecular Sciences 24, no. 1 (2022): 649. http://dx.doi.org/10.3390/ijms24010649.

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Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This researc

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3

Zhu, Lei, Aaron Wenger, Josiah Wilcots, and Primo Baybayan. "Full-length sequencing of CYP2D6 variants with PacBio HiFi reads." Molecular Genetics and Metabolism 132 (April 2021): S275—S276. http://dx.doi.org/10.1016/s1096-7192(21)00507-2.

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4

Callahan, Benjamin. "Amplicon Sequencing in the Era of Highly-Accurate Long Reads." ARPHA Conference Abstracts 4 (March 4, 2021): e65405. https://doi.org/10.3897/aca.4.e65405.

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An important advance in DNA sequencing has been the development of long-read sequencing technologies that produce sequencing reads of tens to hundreds of kilobases in length. However, these technologies typically have high (~8%) per-base error rates. Recently, an effectively new technology I call highly-accurate long-read sequencing has been developed, that allows for the generation of multi-kilobase reads with extremely high per-base accuracies (>99.9%). I will present and evaluate two such technologies, PacBio HiFi and LoopSeq SLR sequencing, and discuss potential metabarcoding applicatio

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Yoo, Byunggil, Ayse Keskus, Chengpeng Bi, et al. "Abstract 1763: Long-read sequencing of pediatric leukemia identifies clinically relevant genomic rearrangements." Cancer Research 84, no. 6_Supplement (2024): 1763. http://dx.doi.org/10.1158/1538-7445.am2024-1763.

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Abstract Clinical detection of genomic rearrangements currently depends on a range of complementary and overlapping methods including fluorescence in situ hybridization (FISH), karyotyping, and DNA and/or RNA sequencing. This requirement for multiple tests results in higher total costs, extended analysis time, and increased usage of sometimes limited tumor material. In our laboratory, we apply long high-fidelity reads to human samples using PacBio circular consensus sequencing (HiFi-GS) of 12-18kb DNA fragments, which offers better structural variant detection relative to short-read sequencing

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6

Javadzadeh, Sara, Aaron Adamson, Jonghun Park, et al. "Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats." PLOS Computational Biology 21, no. 4 (2025): e1012885. https://doi.org/10.1371/journal.pcbi.1012885.

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Variable Number Tandem repeats (VNTRs) refer to repeating motifs of size greater than five bp. VNTRs are an important source of genetic variation, and have been associated with multiple Mendelian and complex phenotypes. However, the highly repetitive structures require reads to span the region for accurate genotyping. Pacific Biosciences HiFi sequencing spans large regions and is highly accurate but relatively expensive. Therefore, targeted sequencing approaches coupled with long-read sequencing have been proposed to improve efficiency and throughput. In this paper, we systematically explored

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7

Volden, Roger, Zev Kronenberg, Aaron Gillmor, et al. "Abstract LB078: pbfusion: Detecting gene-fusion and other transcriptional abnormalities using PacBio HiFi data." Cancer Research 83, no. 8_Supplement (2023): LB078. http://dx.doi.org/10.1158/1538-7445.am2023-lb078.

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Abstract Sarcomas are a broad group of soft tissue and bone cancers that can be difficult to treat leading to a high mortality rate. Sarcomas comprise two broad genomic classes: (1) simple karyotypes, where a single oncogenic structural variant (SV) clonally expands a subtype that is diagnostic and relevant to tumor burden tracking; and (2) complex karyotypes, genomic instability, where SVs continuously arise throughout tumor evolution resulting in heterogeneous cellular subtypes. Class two sarcomas are harder to characterize using genome sequencing because there may be multiple low-frequency

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8

Sockell, Alexandra, Khi Pin Chua, Christopher Kingsley, et al. "Abstract 6624: Comprehensive, multi-omic detection of somatic variants from the GIAB HG008 matched tumor-normal pair using highly accurate long- and short-read whole-genome sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 6624. https://doi.org/10.1158/1538-7445.am2025-6624.

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Abstract Disentangling the molecular drivers of cancer progression requires a precise understanding of the somatic alterations that take place at the DNA level during tumor development. These include not only small changes like SNVs and indels, but also structural variants, changes in repetitive elements, differential methylation, as well as the haplotype context in which these changes occur. Existing short-read sequencing methods using sequencing by synthesis (SBS) chemistry lack the read length to characterize large structural variants or to span longer repetitive regions as well as to phase

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9

Karimi, Karim, Duy Ngoc Do, and Younes Miar. "PSVIII-9 Genome assembly of American mink (Neovison vison) using high-fidelity long reads." Journal of Animal Science 99, Supplement_3 (2021): 241–42. http://dx.doi.org/10.1093/jas/skab235.440.

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Abstract Development of genome-enabled selection and providing new insights in the genetic architecture of economically important traits are essential parts of mink breeding programs. Availability of a contagious genome assembly would guarantee the fundamental genomic studies in American mink (Neovison vison). Advances in long-read sequencing technologies have provided the opportunity to obtain high quality and free-gaps assemblies for different species. The objective of this study was to generate an accurate genome assembly using Single Molecule High-Fidelity (HiFi) Sequencing for American mi

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10

Sun, Jiaman, Jinzhong Zhang, Donald M. Gardiner, et al. "Long-Read Draft Genome Sequences of Two Fusarium oxysporum f. sp. cubense Isolates from Banana (Musa spp.)." Journal of Fungi 11, no. 6 (2025): 421. https://doi.org/10.3390/jof11060421.

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Fusarium oxysporum f. sp. cubense (Foc) causes Fusarium wilt, a devastating epidemic disease that has caused widespread damage to banana crops worldwide. We report the draft genomes of Foc race 1 (16117) and Foc tropical race 4 (Fusarium odoratissimum) (CNSD1) isolates from China, assembled using PacBio HiFi sequencing reads, with functional annotation performed. The strains group in distinct lineages within the Fusarium oxysporum species complex. This genetic resource will contribute towards understanding the pathogenicity and evolutionary dynamics of Foc populations in banana-growing regions

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