Searching journal content for articles similar to Gamaarachchi et al. 34 (5): 778.

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  1. Method: A new compression strategy to reduce the size of nanopore sequencing data
    • Kavindu Jayasooriya,
    • Sasha P. Jenner,
    • Pasindu Marasinghe,
    • Udith Senanayake,
    • Hassaan Saadat,
    • David Taubman,
    • Roshan Ragel,
    • Hasindu Gamaarachchi,
    • and Ira W. Deveson
    Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
    ...of nanopore sequencing signal data with tunable noise parameters. Genome Res 34: 778–783. doi:10.1101/gr.278730.123 ↵Guo Z, Ni Y, Tan L, Shao Y, Ye L, Chen S, Li R. 2024. Nanopore Current Events Magnifier (nanoCEM): a novel tool for visualizing current events at modification sites of nanopore sequencing. NAR...
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  2. Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
    • Alexander Zee,
    • Dori Z.Q. Deng,
    • Matthew Adams,
    • Kayla D. Schimke,
    • Russell Corbett-Detig,
    • Shelbi L. Russell,
    • Xuan Zhang,
    • Robert J. Schmitz,
    • and Christopher Vollmers
    Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
    ...of Illumina sequencers in sequencing core facilities and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer...
  3. Method: Multiplexed long-read plasmid validation and analysis using OnRamp
    • Camille Mumm,
    • Melissa L. Drexel,
    • Torrin L. McDonald,
    • Adam G. Diehl,
    • Jessica A. Switzenberg,
    • and Alan P. Boyle
    Genome Res. May 2023 33: 741-749; Published in Advance May 8, 2023, doi:10.1101/gr.277369.122
    ...detect sequence variation occurring in plasmids from a mixed plasmid pool, we first constructed simulated read data using NanoSim (Yang et al. 2017), a tool designed to simulate nanopore reads. Read libraries were constructed for 30 dissimilar plasmids (average length, 4.4 kb) of known sequence...
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  4. Method: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
    • Pratibha Jagannatha,
    • Alexandra T. Tankka,
    • Daniel A. Lorenz,
    • Tao Yu,
    • Brian A. Yee,
    • Kristopher W. Brannan,
    • Cathy J. Zhou,
    • Jason G. Underwood,
    • and Gene W. Yeo
    Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
    ...sequence (CCS) reads obtained after sequencing were processed using the Iso-Seq v4 pipeline (Epstein et al. 2001; https://isoseq.how/). First, full-length nonconcatemer reads were generated using lima v2.9.0 with the parameter ‐‐isoseq. Reads were then refined with Iso-Seq v4.0.0's refine tool...
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  5. Method: AIDE: annotation-assisted isoform discovery with high precision
    • Wei Vivian Li,
    • Shan Li,
    • Xin Tong,
    • Ling Deng,
    • Hubing Shi,
    • and Jingyi Jessica Li
    Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
    ...and Au 2015) and Oxford Nanopore Technologies (ONT) (Mikheyev and Tin 2014). Even though PacBio and ONT platforms have higher sequencing error rates and lower throughputs compared with second-generation sequencing technologies, they are able to generate much longer reads (1–100 kbp) to simultaneously...
  6. Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
    • Jenna Kalleberg,
    • Jacob Rissman,
    • and Robert D. Schnabel
    Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
    ...for human s (Lloret-Villas et al. 2023). Instead, we tested a range of values for each tunable parameter, resulting in about 300–1000 VQSR runs. From these analyses, we selected VQSR parameter values that produced fewer violations of Mendelian inheritance within bovine trios while increasing the total...
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  7. Method: Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash
    • Mahmudur Rahman Hera,
    • N. Tessa Pierce-Ward,
    • and David Koslicki
    Genome Res. July 2023 33: 1061-1068; Published in Advance June 21, 2023, doi:10.1101/gr.277651.123
    ...) The scale factor s is an easily tunable parameter that can modify the size of the sketch. Using this FracMinHash sketch, we define the FracMinHash estimate of the containment index as follows: (2) Simply speaking, we want to compute because the sketches are considerably smaller than the original sets...
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