Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

DNA sequencing with chain-terminating inhibitors

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Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

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Oryza pan-genomics: A new foundation for future rice research and improvement

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Long-read sequencing on the SMRT platform enables efficient haplotype linkage analysis in preimplantation genetic testing for β-thalassemia

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Pathways to polar adaptation in fishes revealed by long‐read sequencing

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Single-chromosome fission yeast models reveal the configuration robustness of a functional genome

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Legume Pangenome: Status and Scope for Crop Improvement

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Chromosome-Scale Genome Assembly and Annotation of Allotetraploid Annual Bluegrass (Poa annua L.)

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Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes

Zhang, T., Xing, W., Wang, A., Zhang, N., Jia, L., Ma, S., & Xia, Q. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms24010649 · Cited by 22

Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes

Miga, K. H., & Eichler, E. E. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.09.011 · Cited by 23

Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes

Qiu, Z. G., Zhu, Y., Zhang, Q., Qiao, X., Mu, R., Xu, Z., Yan, Y., Wang, F., Zhang, T., Zhuang, W., et al. (2023) · Environmental Science and Ecotechnology · doi:10.1016/j.ese.2023.100359 · Cited by 22

Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri

He, Z., Su, Y., & Wang, T. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020787 · Cited by 22

Phased nanopore assembly with Shasta and modular graph phasing with GFAsePreprint

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Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

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Finding long tandem repeats in long noisy reads

Morishita, S., Ichikawa, K., & Myers, E. W. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa865 · Cited by 22

SKSV: ultrafast structural variation detection from circular consensus sequencing reads

Liu, Y., Jiang, T., Su, J., Liu, B., Zang, T., & Wang, Y. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab341 · Cited by 21

Reconstructing viral haplotypes using long reads

Cai, D., & Sun, Y. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac089 · Cited by 23

Advancing Grain Legumes Domestication and Evolution Studies with Genomics

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Chimera: The spoiler in multiple displacement amplification

Lü, N., Qiao, Y., Lu, Z., & Tu, J. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.02.034 · Cited by 20

Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation

Steyaert, W., Haer‐Wigman, L., Pfundt, R., Hellebrekers, D. M. E. I., Steehouwer, M., Hampstead, J. E., de Boer, E., Stegmann, A. P. A., Yntema, H. G., Kamsteeg, E., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42531-9 · Cited by 20

Defining Blood Group Gene Reference Alleles by Long-Read Sequencing: Proof of Concept in the ACKR1 Gene Encoding the Duffy Antigens

Fichou, Y., Berlivet, I., Richard, G., Tournamille, C., Castilho, L. M., & Férec, C. (2019) · Transfusion Medicine and Hemotherapy · doi:10.1159/000504584 · Cited by 21

High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids

Hu, Y., Ma, D., Ning, S., Qi, Y., Zhao, X.-X., Ding, Q., Liang, P., Cai, G., Ma, X., Qin, X., et al. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.742420 · Cited by 23

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexitiesPreprint

Eisfeldt, J., Ameur, A., Lenner, F., de Boer, E. T. B., Ek, M., Wincent, J., Vaz, R., Ottosson, J., Jonson, T., Ivarsson, S., et al. (2024) · Genome Research · doi:10.1101/gr.279510.124 · Cited by 21

High-throughput and cost-effective genotyping by low-coverage whole genome sequencing with genotype imputation in Pacific oyster, Crassostrea gigas

Yang, B., Li, Y., Li, Q., & Liu, S. (2024) · Aquaculture · doi:10.1016/j.aquaculture.2024.741134 · Cited by 20

Rumen DNA virome and its relationship with feed efficiency in dairy cows

Liu, X., Tang, Y., Chen, H., Liu, J., & Sun, H. (2025) · Microbiome · doi:10.1186/s40168-024-02019-0 · Cited by 20

Multiomic integration reveals subtype-specific predictors of neoadjuvant treatment response in breast cancer

Mo, Z., Yang, M. J., Zhu, Z., Wang, M., Wang, H., Zhang, Z., Lyu, S., Xu, F., Shang, H., Lin, H., et al. (2025) · Science Advances · doi:10.1126/sciadv.adu1521 · Cited by 21

On the complexity of haplotyping a microbial community

Nicholls, S. M., Aubrey, W., Grave, K. D., Schietgat, L., Creevey, C. J., & Clare, A. J. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa977 · Cited by 20

NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology

Wright, I. A., Delaney, K. E., Katusiime, M. G., Botha, J. C., Engelbrecht, S., Kearney, M. F., & van Zyl, G. U. (2021) · Cells · doi:10.3390/cells10102577 · Cited by 20

Concatenation of Transgenic DNA: Random or Orchestrated?

Smirnov, A. V., & Баттулин, Н. Р. (2021) · Genes · doi:10.3390/genes12121969 · Cited by 19

Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes

Ramos, L., & Antunes, A. (2022) · Genomics · doi:10.1016/j.ygeno.2022.110277 · Cited by 19

Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

Yang, X., Zhao, X., Qu, S., Jia, P., Wang, B., Gao, S., Xu, T., Zhang, W., Huang, J., & Ye, K. (2022) · Fundamental Research · doi:10.1016/j.fmre.2022.02.005 · Cited by 19

Intra‐genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing

Sandín, M. M., Romac, S., & Not, F. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.16081 · Cited by 19

Implications of oral streptococcal bacteriophages in autism spectrum disorder

Zhan, T., Zhou, X., Chu, Y., Zhang, T., Zhang, J., Zhao, X., Wang, Z., Ding, R., Meng, Q., Yu, J., et al. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00355-3 · Cited by 20

Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes

Patin, N., & Goodwin, K. D. (2022) · mSystems · doi:10.1128/msystems.00595-22 · Cited by 21

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

Erkes, A., Grove, R., Žarković, M., Krautwurst, S., Koebnik, R., Morgan, R., Wilson, G. G., Hölzer, M., Marz, M., Boch, J., et al. (2023) · BMC Genomics · doi:10.1186/s12864-023-09228-1 · Cited by 24

TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads

Wang, X., Huang, M., Budowle, B., & Ge, J. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1227176 · Cited by 21

RFC1 in an Australasian neurological disease cohort: extending the genetic heterogeneity and implications for diagnostics

Scriba, C. K., Stevanovski, I., Chintalaphani, S. R., Gamaarachchi, H., Ghaoui, R., Ghia, D., Henderson, R. D., Jordan, N., Winkel, A., Lamont, P. J., et al. (2023) · Brain Communications · doi:10.1093/braincomms/fcad208 · Cited by 21

Genomics and conservation: Guidance from training to analyses and applications

Schiebelhut, L. M., Guillaume, A. S., Kuhn, A., Schweizer, R. M., Armstrong, E. E., Beaumont, M., Byrne, M. M., Cosart, T., Hand, B. K., Howard, L., et al. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13893 · Cited by 24

Immune Literacy: Reading, Writing, and Editing Adaptive Immunity

Csepregi, L., Ehling, R. A., Wagner, B., & Reddy, S. T. (2020) · iScience · doi:10.1016/j.isci.2020.101519 · Cited by 22

Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications

Prodanov, T., & Bansal, V. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa829 · Cited by 20

Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici

Samils, B., Andersson, B., Edin, E., Elfstrand, M., Rönneburg, T., Bucur, D., Hutton, F., Heick, T. M., Hellin, P., & Kildea, S. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.692845 · Cited by 20

Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references

Lou, H., Gao, Y., Xie, B., Wang, Y., Zhang, H., Shi, M., Ma, S., Zhang, X., Liu, C., & Xu, S. (2022) · Cell Systems · doi:10.1016/j.cels.2022.01.006 · Cited by 20

TGS-GapCloser: fast and accurately passing through the Bermuda in large genome using error-prone third-generation long readsPreprint

Xu, M., Guo, L., Gu, S., Wang, O., Zhang, R., Fan, G., Xu, X., Deng, L., & Liu, X. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/831248 · Cited by 20

Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotypePreprint

Karl, J. A., Prall, T. M., Bussan, H. E., Varghese, J. M., Pal, A., Wiseman, R. W., & O’Connor, D. H. (2023) · Genome Research · doi:10.1101/gr.277429.122 · Cited by 20

A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-Based Multiple Sequence Alignment

Roe, D., Vierra‐Green, C., Pyo, C., Geraghty, D. E., Spellman, S. R., Maiers, M. J., & Kuang, R. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.585731 · Cited by 19

Next-generation sequencing for the diagnosis of hepatitis B: current status and future prospects

García-García, S., Cortese, M. F., Rodríguez-Algarra, F., Tabernero, D., Rando‐Segura, A., Quer, J., Buti, M., & Rodríguez‐Frias, F. (2021) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2021.1913055 · Cited by 19

Sequencing approaches

Ungelenk, M. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823579-9.00021-7 · Cited by 19

Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange

Wang, Z., Jimenez‐Fernandez, O., Osenbrück, K., Schwientek, M., Schloter, M., Fleckenstein, J. H., & Lueders, T. (2022) · Water Research · doi:10.1016/j.watres.2022.118334 · Cited by 19

Advanced techniques for gene heterogeneity research: Single‐cell sequencing and on‐chip gene analysis systems

Dong, Z., Wang, Y., Yin, D., Hang, X., Pu, L., Zhang, J., Geng, J., & Chang, L. (2022) · Open Research (University of Surrey) · doi:10.1002/viw.20210011 · Cited by 19

TT-Mars: structural variants assessment based on haplotype-resolved assemblies

Yang, J., & Chaisson, M. (2022) · Genome biology · doi:10.1186/s13059-022-02666-2 · Cited by 16

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

Chen, S. H., Martino, A. M., Luo, Z., Schwessinger, B., Jones, A., Tolessa, T. T., Bragg, J. G., Tobias, P. A., & Edwards, R. J. (2022) · GigaScience · doi:10.1093/gigascience/giad102 · Cited by 19

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

Hogg, C. J., Edwards, R. J., Farquharson, K. A., Silver, L. W., Brandies, P. A., Peel, E., Escalona, M., Jaya, F. R., Thavornkanlapachai, R., Batley, K. C., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02436-2 · Cited by 22

HIT-scISOseq: High-throughput and High-accuracy Single-cell Full-length Isoform Sequencing for Corneal EpitheliumPreprint

Zheng, Y., Chen, Z.-C., Shi, Z., Hu, K.-H., Zhong, J., Wang, C., Shi, W., Chen, Y., Xie, S., Luo, F., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.27.222349 · Cited by 18

Semiconservative transmission of DNA N 6 -adenine methylation in a unicellular eukaryotePreprint

Sheng, Y., Wang, Y., Yang, W., Wang, X. Q. D., Lu, J., Pan, B., Nan, B., Liu, Y., Ye, F., Li, C., et al. (2024) · Genome Research · doi:10.1101/gr.277843.123 · Cited by 18

Application of Digital Polymerase Chain Reaction (dPCR) in Non-Invasive Prenatal Testing (NIPT)

Guo, Y. Q., Charoenkwan, P., Traisrisilp, K., Piyamongkol, W., & Tongprasert, F. (2025) · Biomolecules · doi:10.3390/biom15030360 · Cited by 18

Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota

Biada, I., Santacreu, M. A., González-Recio, Ó., & Ibáñez‐Escriche, N. (2025) · Frontiers in Microbiomes · doi:10.3389/frmbi.2025.1587712 · Cited by 18

LUCS: a high-resolution nucleic acid sequencing tool for accurate long-read analysis of individual DNA molecules

Annis, S., Fleischmann, Z., Logan, R. A., Mullin-Bernstein, Z., Franco, M., Saürich, J., Tilly, J. L., Woods, D. C., & Khrapko, K. (2020) · Aging · doi:10.18632/aging.103171 · Cited by 18

Genome-Guided Discovery of Natural Products through Multiplexed Low-Coverage Whole-Genome Sequencing of Soil Actinomycetes on Oxford Nanopore Flongle

Rajwani, R., Ohlemacher, S. I., Zhao, G., Liu, H.-B., & Bewley, C. A. (2021) · mSystems · doi:10.1128/msystems.01020-21 · Cited by 22

A deep dive into genome assemblies of non-vertebrate animals

Guiglielmoni, N., Rivera‐Vicéns, R. E., Koszul, R., & Flot, J. (2022) · Peer Community Journal · doi:10.24072/pcjournal.128 · Cited by 16

Single-Cell DNA Methylation Analysis in Cancer

O’Neill, H., Lee, H. J., Gupta, I., Rodger, E. J., & Chatterjee, A. (2022) · Cancers · doi:10.3390/cancers14246171 · Cited by 19

Benchmarking datasets for assembly-based variant calling using high-fidelity long reads

Lee, H., Kim, J., & Lee, J. (2023) · BMC Genomics · doi:10.1186/s12864-023-09255-y · Cited by 18

Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success

Chen, L., Li, C., Li, B., Zhou, X., Bai, Y., Zou, X., Zhou, Z., He, Q., Chen, B., Wang, M., et al. (2023) · Fundamental Research · doi:10.1016/j.fmre.2023.06.011 · Cited by 18

Recent advances in Alzheimer disease genetics

Nicolas, G. (2024) · Current Opinion in Neurology · doi:10.1097/wco.0000000000001242 · Cited by 19

Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes

Zaccaron, A. Z., & Stergiopoulos, I. (2024) · BMC Biology · doi:10.1186/s12915-024-01818-z · Cited by 17

A comprehensive review of deep learning-based variant calling methods

Junjun, R., Zhengqian, Z., Ying, W., Jialiang, W., & Liu, Y. (2024) · Briefings in Functional Genomics · doi:10.1093/bfgp/elae003 · Cited by 20

Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery

Gao, Z., Lu, Y., Chong, Y., Li, M., Hong, J., Wu, J., Wu, D., Xi, D., & Deng, W. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25137147 · Cited by 19

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Bein, B., Chrysostomakis, I., Arantes, L. S., Brown, T., Gerheim, C., Schell, T., Schneider, C., Leushkin, E. V., Chen, Z., Sigwart, J. D., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03487-9 · Cited by 29

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

Majidian, S., Kahaei, M. H., & de Ridder, D. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03584-5 · Cited by 18

Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads

Zhou, X., Zhang, L., Weng, Z., Dill, D., & Sidow, A. (2021) · Nature Communications · doi:10.1038/s41467-021-21395-x · Cited by 16

Genomic region associated with pod color variation in pea ( Pisum sativum )

Shirasawa, K., Sasaki, K., Hirakawa, H., & Isobe, S. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab081 · Cited by 18

Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

Lopes, M., Louzada, S., Gama‐Carvalho, M., & Chaves, R. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094707 · Cited by 19

CoLoRd: compressing long reads

Kokot, M., Gudyś, A., Li, H., & Deorowicz, S. (2022) · Nature Methods · doi:10.1038/s41592-022-01432-3 · Cited by 18

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source toolsPreprint

Monat, C., Padmarasu, S., Lux, T. M., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G. J., Schulman, A. H., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/631648 · Cited by 18

Chromosome-level genome assembly of Nibea coibor using PacBio HiFi reads and Hi-C technologies

Yekefenhazi, D., He, Q., Wang, X., Han, W. J., Song, C., & Li, W. (2022) · Scientific Data · doi:10.1038/s41597-022-01804-6 · Cited by 17

Telomere-to-telomere genome assembly of the goose Anser cygnoides

Zhao, H., Zhou, H., Sun, G., Dong, B., Zhu, W., Mu, X., Li, X., Wang, J., Zhao, M., Yang, W., et al. (2024) · Scientific Data · doi:10.1038/s41597-024-03567-8 · Cited by 21

A Hitchhiker's Guide to long-read genomic analysisPreprint

Mahmoud, M., Agustinho, D. P., & Sedlazeck, F. J. (2025) · Genome Research · doi:10.1101/gr.279975.124 · Cited by 22

Development and establishment of oral microbiota in early life

Kageyama, S., & Takeshita, T. (2024) · Journal of Oral Biosciences · doi:10.1016/j.job.2024.05.001 · Cited by 19

Long-read genome sequencing resolves complex genomic rearrangements in rare genetic syndromes

Showpnil, I. A., Hernandez‐Gonzalez, M. E., Ramadesikan, S., Marhabaie, M., Daley, A., Dublin-Ryan, L., Pastore, M., Umamaheswaran, G., Hunter, J. M., Stone, B. S., et al. (2024) · npj Genomic Medicine · doi:10.1038/s41525-024-00454-4 · Cited by 18

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Schell, T., Greve, C., & Podsiadłowski, L. (2025) · Frontiers in Zoology · doi:10.1186/s12983-025-00561-7 · Cited by 24

Single-cell omics sequencing technologies: the long-read generation

Wen, L., & Tang, F. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.07.012 · Cited by 18

Pathogenic 12-kb copy-neutral inversion in syndromic intellectual disability identified by high-fidelity long-read sequencing

Mizuguchi, T., Okamoto, N., Yanagihara, K., Miyatake, S., Uchiyama, Y., Tsuchida, N., Hamanaka, K., Fujita, A., Miyake, N., & Matsumoto, N. (2020) · Genomics · doi:10.1016/j.ygeno.2020.10.038 · Cited by 16

A Genome forBidens hawaiensis: A Member of a Hexaploid Hawaiian Plant Adaptive Radiation

Bellinger, M. R., Datlof, E. M., Selph, K. E., Gallaher, T. J., & Knope, M. L. (2021) · Journal of Heredity · doi:10.1093/jhered/esab077 · Cited by 19

Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis

Rai, A., Hirakawa, H., Rai, M., Shimizu, Y., Shirasawa, K., Kikuchi, S., Seki, H., Yamazaki, M., Toyoda, A., Isobe, S., et al. (2022) · DNA Research · doi:10.1093/dnares/dsac043 · Cited by 19

From gene to dose: Long-read sequencing and *-allele tools to refine phenotype predictions of CYP2C19

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Article Watch: March, 2020

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