Searching journal content for articles similar to Antipov et al. 35 (7): 1583.

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  1. Method: Telomere-to-telomere assembly by preserving contained reads
    • Sudhanva Shyam Kamath,
    • Mehak Bindra,
    • Debnath Pal,
    • and Chirag Jain
    Genome Res. November 2024 34: 1908-1918; Published in Advance October 15, 2024, doi:10.1101/gr.279311.124
    ...Bruijn graph-based assemblers and, as such, do not share the limitations of contained read deletion caused in the string graph-based assemblers like hifiasm.We expected improvements in the data sets comprising ONT reads (D2–D4) because these data sets have wide read-length distributions (Supplemental Fig...
  2. Method: Long-read reconstruction of many diverse haplotypes with devider
    • Jim Shaw,
    • Christina Boucher,
    • Yun William Yu,
    • Noelle Noyes,
    • and Heng Li
    Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
    ...techniques. Here, we present devider, an algorithm for haplotyping small sequences, such as viruses or genes, from long-read sequencing. devider uses a positional de Bruijn graph with sequence-to-graph alignment on an alphabet of informative alleles to provide a fast assembly-inspired approach compatible...
  3. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...Bio) and Oxford Nanopore Technologies (ONT) are revolutionizing genomics: They are making chromosome-level assemblies routine, and full diploid, telomere-to-telomere (T2T) assemblies are becoming the standard for human assemblies. LRS employs single-molecule sequencing, avoiding many biases, errors...
  4. Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
    • William J. Murphy and
    • Andrew J. Harris
    Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
    ...; Lescroart et al. 2023). Heatmaps of contig (left) and scaffold (right) N50 metrics are shown from the highest-quality reference s from each respective species. Genomes nearing telomere-to-telomere (T2T) status are represented as assemblies with high contig and scaffold N50's (i.e., domestic cat), whereas...
  5. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...has been instrumental in recent breakthroughs in understanding complex genomic regions and epigenetic regulation. The Telomere-to-Telomere (T2T) consortium (Nurk et al. 2022) demonstrated the power of these technologies by resolving previously intractable regions of the human . In particular, long...
  6. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...discuss how the telomere-to-telomere and the emerging human pan could enhance the resolution of cancer analysis, potentially revolutionizing early detection and disease monitoring in patients. Finally, we outline strategies for transitioning long-read sequencing from research applications to routine...
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  7. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    ...: phase 2 data release and analysis of R9.0 chemistry. F1000Res 6: 760. doi:10.12688/f1000research.11354.1 ↵Johnson J, Soehnlen M, Blankenship HM. 2023. Long read assemblers struggle with small plasmids. Microb Genom 9: mgen001024. doi:10.1099/mgen.0.001024 ↵Jolley KA, Maiden MCJ. 2010. BIGSdb: scalable...
  8. Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
    • Brianna Chrisman,
    • Chloe He,
    • Jae-Yoon Jung,
    • Nate Stockham,
    • Kelley Paskov,
    • Peter Washington,
    • Juli Petereit,
    • and Dennis P. Wall
    Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
    ...the next official human reference . The T2T-CHM13 assembly relies on high-fidelity long-read sequencing (HiFi sequencing) and on novel graph-based algorithms for stitching reads together (Nurk et al. 2022). Our localizations rely on short-read sequencing and a novel maximum likelihood algorithm that uses...
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  9. Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
    • Nathan Hammond,
    • Linda Liao,
    • Pun Wai Tong,
    • Zena Ng,
    • Thuy-Mi P. Nguyen,
    • Chandler Ho,
    • Yao Yang,
    • and Stuart A. Scott
    Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
    ...benefit of variant phasing (Ardui et al. 2018; Ameur et al. 2019). The two primary long-read sequencing chemistries currently available are single molecule real-time (SMRT; HiFi) and nanopore sequencing, which recently have been employed by the Telomere-to-Telomere (T2T) Consortium to more comprehensively...
  10. Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
    • Rita Tam,
    • Mareike Möller,
    • Runpeng Luo,
    • Zhenyan Luo,
    • Ashley Jones,
    • Sambasivam Periyannan,
    • John P. Rathjen,
    • and Benjamin Schwessinger
    Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
    ...Agriculture and Food, Canberra ACT 2601, Australia; 3School of Agriculture and Environmental Science, Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4350, Australia Corresponding authors: john.rathjen@anu.edu.au, benjamin.schwessinger@anu.edu.auAbstractPhased telomere-to-telomere...
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