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Journal articles on the topic 'PacBio HiFi sequencing'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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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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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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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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11

Chen, Xiao, Egor Dolzhenko, Emily Farrow, et al. "P819: Genome-wide resolution of highly homologous genes using long-read PacBio HiFi sequencing*." Genetics in Medicine Open 2 (2024): 101730. http://dx.doi.org/10.1016/j.gimo.2024.101730.

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12

Krautwurst, Melina, Annika Eikhof, Sylke Winkler, Daniel Bross, Birgit Kersten, and Niels A. Müller. "High-molecular-weight DNA extraction for broadleaved and conifer tree species." Silvae Genetica 73, no. 1 (2024): 85–98. http://dx.doi.org/10.2478/sg-2024-0009.

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Abstract Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step in these genome projects is the successful extraction of high-molecular-weight DNA in high quality and sufficient quantity, which is imperative for long-read sequencing. The extraction of high-molecular-weight DNA in trees has been limited and difficult to conduct. To achieve successful extraction, modification of the protocol for tree species is necessary. Here, we present a protocol for high-molecular-weight DNA extraction from the broadleaved tree species F

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Jackson, Christopher J., Todd G. B. McLay, Gareth D. Holmes, Theodore R. Allnutt, and Alastair S. Robinson. "A high quality genome of the common swamp pitcher plant (Nepenthes mirabilis) using PacBio HiFi sequencing." PLOS One 20, no. 7 (2025): e0322885. https://doi.org/10.1371/journal.pone.0322885.

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The genus Nepenthes, known commonly as tropical pitcher plants, are amongst the most recognisable carnivorous plants, capturing and digesting organic material in highly modified ‘pitcher’ leaves to acquire nitrogen and other valuable nutrients that are naturally scarce in their habitats. Here, PacBio HiFi long-read sequencing was used to assemble a near chromosome-level genome for a female specimen of Nepenthes mirabilis. We compare the genome organisation and gene content with a recently published chromosome-level assembly from a male specimen of the closely related N. gracilis, generated usi

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14

Han, Tina, Holly Corbitt, Egor Dolzhenko, et al. "P478: Simultaneous analysis of 50+ different repeat expansions with twist target enrichment and PacBio HiFi sequencing." Genetics in Medicine Open 1, no. 1 (2023): 100525. http://dx.doi.org/10.1016/j.gimo.2023.100525.

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15

Rodriguez Ruiz, Alfredo, and Alex R. Van Dam. "Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains." PeerJ 11 (November 22, 2023): e16276. http://dx.doi.org/10.7717/peerj.16276.

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PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed bacterial contamination within intragenic regions of Arthropoda binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07 Gb genome c

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16

Hogg, Grant, Kimberly A. Holden, John Howitt, et al. "Abstract 679: Orthogonal confirmation using the Pacbio®two step universal adapter amplicon protocol to validate a comprehensive genomic profiling assay for hematologic malignancies." Cancer Research 85, no. 8_Supplement_1 (2025): 679. https://doi.org/10.1158/1538-7445.am2025-679.

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Abstract Next generation sequencing (NGS) using targeted panels is standard of care to aid diagnosis, prognosis and treatment selection for hematologic diseases such as acute myeloid leukemia. We have validated the Labcorp Pan-Heme NGS (LPH) panel that targets 141 clinically relevant genes to detect single nucleotide variants (SNVs), insertions/deletions (indels), FLT3 internal tandem duplicates (FLT3-ITDs) and copy number aberrations (CNAs) in myeloid and lymphoid malignancies. In total, 677 samples were assessed including 315 clinical samples. Analytical sensitivity and specificity experimen

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Chua, Khi Pin, Ian McLaughlin, Oliver Hofmann, et al. "Abstract 2934: Somatic variant workflow with HiFi sequencing provides new insights in highly challenging cancer cases." Cancer Research 84, no. 6_Supplement (2024): 2934. http://dx.doi.org/10.1158/1538-7445.am2024-2934.

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Abstract Tumor evolution is a highly heterogeneous process where multiple oncogenic pathways can lead to host defense evasion. Advancements in genome sequencing are allowing us to better understand these processes and their impact. However, critical genomic variations that could be pivotal to the development of tumors may have remained undetected due to technological constraints of short-read sequencing. PacBio HiFi sequencing generates accurate (&gt;99.9%) long reads (&gt;15 kb) with native 5-methylcytosine information that can comprehensively delineate many variations, including ones

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Bono, Hidemasa. "Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing." International Journal of Molecular Sciences 26, no. 7 (2025): 3442. https://doi.org/10.3390/ijms26073442.

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Genome-editing technology has advanced significantly since the 2020 Nobel Prize in Chemistry was awarded for the development of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9). While CRISPR–Cas9 has become widely used in academic research, its social implementation has lagged due to unresolved patent disputes and slower progress in gene function analysis. To address this, new approaches bypassing direct gene function analysis are needed, with bioinformatics and next-generation sequencing (NGS) playing crucial roles. NGS is essential for

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Cosma, Bianca-Maria, Ramin Shirali Hossein Zade, Erin Noel Jordan, et al. "Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations." GigaScience 12 (December 28, 2022). http://dx.doi.org/10.1093/gigascience/giad100.

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Abstract Background Assembly algorithm choice should be a deliberate, well-justified decision when researchers create genome assemblies for eukaryotic organisms from third-generation sequencing technologies. While third-generation sequencing by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) has overcome the disadvantages of short read lengths specific to next-generation sequencing (NGS), third-generation sequencers are known to produce more error-prone reads, thereby generating a new set of challenges for assembly algorithms and pipelines. However, the introduction of HiFi

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20

Zhu, Liya, Céline Lopez-Roques, Marine Sallaberry, et al. "Whole-genome sequences of 38 siderophore-producing isolates from root systems of two pea and one wheat varieties." Microbiology Resource Announcements, July 23, 2025. https://doi.org/10.1128/mra.00570-25.

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ABSTRACT Here, we report the whole-genome sequencing of 38 siderophore-producing bacterial strains isolated from the root systems of two pea and one wheat varieties. High-quality genomic data for each isolate was generated using PacBio HiFi sequencing, producing 6.1 Gb of HiFi reads and achieving an average assembly completeness of 98.85%.

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Denti, Luca, Parsoa Khorsand, PAOLA BONIZZONI, Fereydoun Hormozdiari, and Rayan Chikhi. "SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads." Nature Methods 20 (December 22, 2022). https://doi.org/10.5281/zenodo.15086046.

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Structural variants (SVs) account for a large amount of sequence variability across genomes and play an important role in human genomics and precision medicine. Despite intense efforts over the years, the discovery of SVs in individuals remains challenging due to the diploid and highly repetitive structure of the human genome, and by the presence of SVs that vastly exceed sequencing read lengths. However, the recent introduction of low-error long-read sequencing technologies such as PacBio HiFi may finally enable these barriers to be overcome. Here we present SV discovery with sample-specific

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Bronner, Iraad F., Emma Dawson, Naomi Park, Olaf Piepenburg, and Michael A. Quail. "Evaluation of controls, quality control assays, and protocol optimisations for PacBio HiFi sequencing on diverse and challenging samples." Frontiers in Genetics 15 (January 6, 2025). https://doi.org/10.3389/fgene.2024.1505839.

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The Darwin Tree of Life (DToL) project aims to generate high-quality reference genomes for all eukaryotic organisms in Britain and Ireland. At the time of writing, PacBio HiFi reads are generated for all samples using the Sequel IIe systems by the Wellcome Sanger Institute’s Scientific Operations teams, however we expect lessons from this work to apply directly to the Revio system too, as core principles of SMRT sequencing remain the same. We observed that HiFi yield is highly variable for DToL samples. We have investigated what drives this variation, and potential mitigations. To support thes

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Weerakoon, Minindu, Sangjin Lee, Emily Mitchell, and Haynes Heaton. "TopoQual polishes circular consensus sequencing data and accurately predicts quality scores." BMC Bioinformatics 26, no. 1 (2025). https://doi.org/10.1186/s12859-024-06020-0.

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Abstract Background Pacific Biosciences (PacBio) circular consensus sequencing (CCS), also known as high fidelity (HiFi) technology, has revolutionized modern genomics by producing long (10 + kb) and highly accurate reads. This is achieved by sequencing circularized DNA molecules multiple times and combining them into a consensus sequence. Currently, the accuracy and quality value estimation provided by HiFi technology are more than sufficient for applications such as genome assembly and germline variant calling. However, there are limitations in the accuracy of the estimated quality scores wh

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Zhang, Zhiliang, Jijin Zhang, Lipeng Kang, et al. "Structural variation discovery in wheat using PacBio high‐fidelity sequencing." Plant Journal, September 6, 2024. http://dx.doi.org/10.1111/tpj.17011.

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SUMMARYStructural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed due to their complex nature and the limitations of early genomic technologies. By applying the PacBio high‐fidelity (HiFi) sequencing for wheat genomes, we performed a comprehensive evaluation of mainstream long‐read aligners and SV callers in SV detection. The results indicated that the accuracy of deletion discovery is markedly influenced by callers, accounting for 87.73% of the variance, whereas both aligners (38.25%) and callers (49

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Nishii, Kanae, Michael Möller, Robert G. Foster, et al. "A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants." Plant Methods 19, no. 1 (2023). http://dx.doi.org/10.1186/s13007-023-01009-x.

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Abstract Background PacBio HiFi sequencing provides highly accurate long-read sequencing datasets which are of great advantage for whole genome sequencing projects. One limitation of the method is the requirement for high quality, high molecular weight input DNA. This can be particularly challenging for plants that frequently contain common and species-specific secondary metabolites, which often interfere with downstream processes. Cape Primroses (genus Streptocarpus), are some of these recalcitrant plants and are selected here as material to develop a high quality, high molecular weight DNA e

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Fan, Jiang. "Metagenome-assembled microbial genomes by PacBio high-fidelity sequencing." November 11, 2022. https://doi.org/10.5281/zenodo.7312333.

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we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥ 18 types of standard tRNA genes, and 39 are circular complete genomes.

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Tvedte, Eric S., Mark Gasser, Benjamin C. Sparklin, et al. "Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes." G3 Genes|Genomes|Genetics 11, no. 6 (2021). http://dx.doi.org/10.1093/g3journal/jkab083.

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Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit f

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Abdel-Hamid, Ahmed M., Taylor Putman, Megan Furukawa, et al. "Complete genome sequence of Methylocystis echinoides strain RIM isolated from soil." Microbiology Resource Announcements, February 25, 2025. https://doi.org/10.1128/mra.01155-24.

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ABSTRACT We report here the complete genome sequence of a type II methanotrophic bacterium, Methylocystis echinoides strain RIM, isolated from the soil surface at Urbana, Illinois. This genome was obtained via HiFi PacBio Sequel II sequencing.

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Wang, Bo, Peng Jia, Shenghan Gao, et al. "Long and Accurate: How HiFi Sequencing is Transforming Genomics." Genomics, Proteomics & Bioinformatics, February 7, 2025. https://doi.org/10.1093/gpbjnl/qzaf003.

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Abstract Recent developments in PacBio high-fidelity (HiFi) sequencing technologies have transformed genomic research, with circular consensus sequencing now achieving 99.9% accuracy for long (up to 25 kb) single-molecule reads. This method circumvents biases intrinsic to amplification-based approaches, enabling thorough analysis of complex genomic regions [including tandem repeats, segmental duplications, ribosomal DNA (rDNA) arrays, and centromeres] as well as direct detection of base modifications, furnishing both sequence and epigenetic data concurrently. This has streamlined a number of t

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Miranda, Jaime A., and Javier R. Revollo. "Assessment of In Vivo Chemical Mutagenesis by Long-Read Sequencing." Toxicological Sciences, August 14, 2024. http://dx.doi.org/10.1093/toxsci/kfae104.

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Abstract Evaluating the mutagenic properties of chemicals is crucial for understanding their potential cancer risks. Recent Illumina-based error-corrected sequencing techniques have enabled the direct detection of mutations induced de novo by mutagens. However, as the Illumina platform lacks intrinsic error-correction capabilities, complex library preparations and bioinformatic processes are necessary to identify these rare mutations. In this study, we evaluated whether long-read PacBio-based HiFi sequencing (HiFi seq), which has integrated error-correction, can detect de novo mutations induce

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Kraege, A., BPHJ Thomma, and H. Rovenich. "Fastqc reports of sequencing data from Coccomyxa viridis SAG 216-4." June 27, 2023. https://doi.org/10.5281/zenodo.8084901.

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Here we provide access to the fastqc files of the corresponding PacBio Hifi, ONT, Hi-C and RNAseq data that were used to generate a high-quality chromosome-scale genome assembly and annotation for the eukaryotic terrestrial alga <em>Coccomyxa viridis </em>SAG 216-4.

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Biada, Iliyass, María Antonia Santacreu, Oscar González-Recio, and Noelia Ibáñez-Escriche. "Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota." Frontiers in Microbiomes 4 (May 15, 2025). https://doi.org/10.3389/frmbi.2025.1587712.

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This research aims to assess whether sequencing the full length of the 16S rRNA gene using PacBio HiFi sequencing and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. Moreover, it aims to compare the similarities in microbial communities detected across the three platforms. The study employed DNA from four rabbit does’ soft feces, sequenced using Illumina MiSeq for specific 16S rRNA gene regions V3-V4, and for the complete gene sequencing using PacBio HiFi and ONT MinION. Results highlight different levels of taxonomic r

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Lang, Dandan, Shilai Zhang, Pingping Ren, et al. "Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore." GigaScience 9, no. 12 (2020). http://dx.doi.org/10.1093/gigascience/giaa123.

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Abstract Background The availability of reference genomes has revolutionized the study of biology. Multiple competing technologies have been developed to improve the quality and robustness of genome assemblies during the past decade. The 2 widely used long-read sequencing providers—Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)—have recently updated their platforms: PacBio enables high-throughput HiFi reads with base-level resolution of &gt;99%, and ONT generated reads as long as 2 Mb. We applied the 2 up-to-date platforms to a single rice individual and then compared

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Hon, Ting, Kristin Mars, Greg Young, et al. "Highly accurate long-read HiFi sequencing data for five complex genomes." Scientific Data 7, no. 1 (2020). http://dx.doi.org/10.1038/s41597-020-00743-4.

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AbstractThe PacBio® HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemble

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Sim, Sheina B., Renee L. Corpuz, Tyler J. Simmonds, and Scott M. Geib. "HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly." BMC Genomics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12864-022-08375-1.

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Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is ne

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Hu, Jiang, Zhuo Wang, Fan Liang, Shan-Lin Liu, Kai Ye, and De-Peng Wang. "NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads." Genomics, Proteomics & Bioinformatics, January 4, 2024. http://dx.doi.org/10.1093/gpbjnl/qzad009.

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Abstract The high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies. However, these assemblies still contain base-level errors, particularly within the error-prone regions of HiFi long reads. Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads. Here we describe an upgraded genome polishing tool–NextPolish2, which can fix base errors remaining in those “highly accurate” genomes assembled from HiFi long read

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Wang, Xuewen, Melissa Muenzler, Jonathan King, et al. "A complete pipeline enables haplotyping and phasing macrohaplotype in long sequencing reads for polyploidy samples and a multi‐source DNA mixture." ELECTROPHORESIS, January 9, 2024. http://dx.doi.org/10.1002/elps.202300143.

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AbstractMacrohaplotype combines multiple types of phased DNA variants, increasing forensic discrimination power. High‐quality long‐sequencing reads, for example, PacBio HiFi reads, provide data to detect macrohaplotypes in multiploidy and DNA mixtures. However, the bioinformatics tools for detecting macrohaplotypes are lacking. In this study, we developed a bioinformatics software, MacroHapCaller, in which targeted loci (i.e., short TRs [STRs], single nucleotide polymorphisms, and insertion and deletions) are genotyped and combined with novel algorithms to call macrohaplotypes from long reads.

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Richy, Etienne, Priscila Thiago Dobbler, Vojtěch Tláskal, Rubén López-Mondéjar, Petr Baldrian, and Martina Kyselková. "Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes." Environmental Microbiome 19, no. 1 (2024). https://doi.org/10.1186/s40793-024-00639-5.

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Abstract Background Deadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood. Results Here, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved tr

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Guo, Yujie, Xiaowen Feng, and Heng Li. "Evaluation of haplotype-aware long-read error correction with hifieval." Bioinformatics, October 18, 2023. http://dx.doi.org/10.1093/bioinformatics/btad631.

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Abstract Summary The PacBio High-Fidelity (HiFi) sequencing technology produces long reads of &gt; 99% in accuracy. It has enabled the development of a new generation of de novo sequence assemblers, which all have sequencing error correction as the first step. As HiFi is a new data type, this critical step has not been evaluated before. Here, we introduced hifieval, a new command-line tool for measuring over- and under-corrections produced by error correction algorithms. We assessed the accuracy of the error correction components of existing HiFi assemblers on the CHM13 and the HG002 datas

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Okumura, Leonardo Ken, and Shinji Masuda. "Complete genome sequence of Synechocystis sp. LKSZ1 isolated from a pond in the Suzukakedai campus of Tokyo Institute of Technology." Microbiology Resource Announcements, September 9, 2024. http://dx.doi.org/10.1128/mra.00549-24.

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ABSTRACT Cyanobacteria belonging to the Synechocystis genus have been isolated from diverse aquatic environments. This announcement reports the complete genome sequence of Synechocystis sp. LKSZ1 newly isolated from a pond in a university campus in Yokohama, Japan. The genome sequencing was performed using the PacBio Revio HiFi long-read technology.

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Ángel C., Carlos A., Gustavo A. Marín-Ramírez, and Carlos E. Maldonado. "Genome sequence of Hemileia vastatrix Berk. and Br. (Race I), the causal agent of coffee leaf rust, isolate from Risaralda, Colombia." Microbiology Resource Announcements, October 4, 2023. http://dx.doi.org/10.1128/mra.00444-23.

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ABSTRACT Coffee leaf rust, caused by the fungus Hemileia vastatrix (Basidiomycota; Pucciniomycota) , is a devastating disease spread worldwide. To improve the available genomes, we use PacBio HiFi sequencing enhanced by Dovetail Omni-C chromatin conformation capture to assemble a highly contiguous 747.98 Mb genome of an isolate collected from Coffea arabica .

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Wang, Jingjing, Werner Pieter Veldsman, Xiaodong Fang, et al. "Benchmarking multi-platform sequencing technologies for human genome assembly." Briefings in Bioinformatics, August 18, 2023. http://dx.doi.org/10.1093/bib/bbad300.

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Abstract Genome assembly is a computational technique that involves piecing together deoxyribonucleic acid (DNA) fragments generated by sequencing technologies to create a comprehensive and precise representation of the entire genome. Generating a high-quality human reference genome is a crucial prerequisite for comprehending human biology, and it is also vital for downstream genomic variation analysis. Many efforts have been made over the past few decades to create a complete and gapless reference genome for humans by using a diverse range of advanced sequencing technologies. Several availabl

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Niu, Yongchao, Xinhao Fan, Yalan Yang, et al. "Haplotype-resolved assembly of a pig genome using single-sperm sequencing." Communications Biology 7, no. 1 (2024). http://dx.doi.org/10.1038/s42003-024-06397-x.

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AbstractSingle gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was developed based on long-read sequencing and sperm-phased markers. The chromosome-level phased assembly showed higher phasing accuracy than methods that rely only on HiFi reads. The use of single-sperm sequencing data enabled the construction of a genetic map, successfully mapping the sperm motili

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Plaza Oñate, Florian, Hugo Roume, and Mathieu Almeida. "Recovery of Metagenome-Assembled Genomes from a Human Fecal Sample with Pacific Biosciences High-Fidelity Sequencing." Microbiology Resource Announcements, May 9, 2022. http://dx.doi.org/10.1128/mra.00250-22.

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Here, we report the recovery of 89 metagenome-assembled genomes (MAGs) derived from a human fecal sample subjected to Pacific Biosciences (PacBio) high-fidelity (HiFi) sequencing. A total of 9 MAGs consisted of complete circular contigs, and 45 MAGs were high-quality draft genomes according to the minimum information about a metagenome-assembled genome (MIMAG) standards.

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Alami, Mohammad Murtaza, Shaohua Shu, Sanbo Liu, et al. "Chromosome-scale genome assembly of medicinal plant Tinospora sagittata (Oliv.) Gagnep. from the Menispermaceae family." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03315-y.

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AbstractTinospora sagittata (Oliv.) Gagnep. is an important medicinal tetraploid plant in the Menispermaceae family. Its tuber, Radix Tinosporae, used in traditional Chinese medicine, is rich in diterpenoids and benzylisoquinoline alkaloids (BIAs). To enhance our understanding of medicinal compounds’ biosynthesis and Menispermaceae’s evolution, we herein report assembling a high-quality chromosome-scale genome with both PacBio HiFi and Illumina sequencing technologies. PacBio Sequel II generated 2.5 million circular consensus sequencing (CCS) reads, and a hybrid assembly strategy with Illumina

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Yu, Wenjuan, Haohui Luo, Jinbao Yang, et al. "Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes." Genome Research, March 1, 2024. http://dx.doi.org/10.1101/gr.278232.123.

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Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data set

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Portik, Daniel M., C. Titus Brown, and N. Tessa Pierce-Ward. "Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets." BMC Bioinformatics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12859-022-05103-0.

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Abstract Background Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and profiling. The development of long-read specific tools for taxonomic classification is accelerating, yet there is a lack of information regarding their relative performance. Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to

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Núñez-Rodríguez, Lester A., Catherine L. Wram, Cedar Hesse, and Inga A. Zasada. "Genome Announcement: Draft Genome Assembly of Heterodera humuli Generated Using Long-Read Sequencing." Journal of Nematology 56, no. 1 (2024). http://dx.doi.org/10.2478/jofnem-2024-0029.

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Abstract The hop cyst nematode, Heterodera humuli, is the most common plant-parasitic nematode associated with hop worldwide. This study reports the draft genome of H. humuli generated on the PacBio Sequel IIe System with the ultra-low DNA input HiFi sequencing method, and the corresponding genome annotation. This genome resource will help further studies on H. humuli and other cyst nematodes.

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Kucuk, Erdi, Bart P. G. H. van der Sanden, Luke O’Gorman, et al. "Comprehensive de novo mutation discovery with HiFi long-read sequencing." Genome Medicine 15, no. 1 (2023). http://dx.doi.org/10.1186/s13073-023-01183-6.

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Abstract Background Long-read sequencing (LRS) techniques have been very successful in identifying structural variants (SVs). However, the high error rate of LRS made the detection of small variants (substitutions and short indels < 20 bp) more challenging. The introduction of PacBio HiFi sequencing makes LRS also suited for detecting small variation. Here we evaluate the ability of HiFi reads to detect de novo mutations (DNMs) of all types, which are technically challenging variant types and a major cause of sporadic, severe, early-onset disease. Methods We sequenced the genomes of eight p

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Uliano-Silva, Marcela, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, et al. "MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads." BMC Bioinformatics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12859-023-05385-y.

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Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. Results MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input

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