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<p>Long-read RNA sequencing is a powerful technology to link transcript structures to genetic variants, but this type of analysis is not often performed owing to the lack of end-user tools. Here we introduce longcallR for joint single-nucleotide polymorphism calling, haplotype phasing and allele-specific analysis, which achieves high accuracy on benchmark datasets. Applied to 202 human samples, longcallR identified 88 significant allele-specific splicing events per sample on average, of which 46% involved unannotated junctions.</p>

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SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads

  • 期刊论文

  • 发表日期：

    2026年3月30日

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  • Neng Huang,
  • Heng Li,
  • Ahmad Abou Tayoun,
  • Derek Albracht,
  • Jamie Allen,
  • Alawi A. Alsheikh-Ali,
  • Casey Andrews,
  • Dmitry Antipov,
  • Lucinda Antonacci-Fulton,
  • Mobin Asri,
  • Marcelo Ayllon,
  • Jennifer R. Balacco,
  • Floris P. Barthel,
  • Edward A. Belter Jr,
  • Halle D. Bender,
  • Andrew P. Blair,
  • Silvia Buonaiuto,
  • Davide Bolognini,
  • Katherine E. Bonini,
  • Christina Boucher,
  • Guillaume Bourque,
  • Shuo Cao,
  • Andrew Carroll,
  • Ann M. Mc Cartney,
  • Monika Cechova,
  • Pi-Chuan Chang,
  • Xian Chang,
  • Jitender Cheema,
  • Haoyu Cheng,
  • Claudio Ciofi,
  • Sarah Cody,
  • Vincenza Colonna,
  • Holland C. Conwell,
  • Robert Cook-Deegan,
  • Mark Diekhans,
  • Maria Angela Diroma,
  • Daniel Doerr,
  • Zheng Dong,
  • Richard Durbin,
  • Jana Ebler,
  • Evan E. Eichler,
  • Jordan M. Eizenga,
  • Parsa Eskandar,
  • Eddie Ferro,
  • Anna-Sophie Fiston-Lavier,
  • Sarah M. Ford,
  • Willard W. Ford,
  • Giulio Formenti,
  • Adam Frankish,
  • Mallory A. Freeberg,
  • Qichen Fu,
  • Stephanie M. Fullerton,
  • Robert S. Fulton,
  • Yan Gao,
  • Gage H. Garcia,
  • Obed A. Garcia,
  • Joshua M. V. Gardner,
  • Shilpa Garg,
  • Erik Garrison,
  • Nanibaa’ A. Garrison,
  • John Garza,
  • Margarita Geleta,
  • Mohammadmersad Ghorbani,
  • Tina Graves-Lindsay,
  • Richard E. Green,
  • Cristian Groza,
  • Andrea Guarracino,
  • Melissa Gymrek,
  • Leanne Haggerty,
  • Ira M. Hall,
  • Nancy F. Hansen,
  • Mohammad Amiruddin Hashmi,
  • Maximilian Haeussler,
  • Yue Hao,
  • David Haussler,
  • Prajna Hebbar,
  • Peter Heringer,
  • Glenn Hickey,
  • Todd L. Hillaker,
  • S. Nakib Hossain,
  • Sarah E. Hunt,
  • Toby Hunt,
  • Alexander G. Ioannidis,
  • Nafiseh Jafarzadeh,
  • Nivesh Jain,
  • Erich D. Jarvis,
  • Maryam Jehangir,
  • Juan Jiang,
  • Jonathan LoTempio Jr,
  • Eimear E. Kenny,
  • Juhyun Kim,
  • Bonhwang Koo,
  • Sergey Koren,
  • Milinn Kremitzki,
  • Ben Langmead,
  • Xiaoyu Zhuo,
  • Heather A. Lawson,
  • Daofeng Li,
  • Wen-Wei Liao,
  • Jiadong Lin,
  • Tianjie Liu,
  • Glennis A. Logsdon,
  • Ryan Lorig-Roach,
  • Hailey Loucks,
  • Jane E. Loveland,
  • Jianguo Lu,
  • Shuangjia Lu,
  • Julian K. Lucas,
  • Juan F. Macias-Velasco,
  • Maximillian G. Marin,
  • Franco L. Marsico,
  • Kateryna D. Makova,
  • Christopher Markovic,
  • Tobias Marschall,
  • Fergal J. Martin,
  • Mira Mastoras,
  • Capucine Mayoud,
  • Brandy McNulty,
  • Jack A. Medico,
  • Julian M. Menendez,
  • Karen H. Miga,
  • Anna Minkina,
  • Matthew W. Mitchell,
  • Saswat K. Mohanty,
  • Younes Mokrab,
  • Jean Monlong,
  • Shabir Moosa,
  • Avelina Moreno-Ochando,
  • Shinichi Morishita,
  • Jonathan M. Mudge,
  • Katherine M. Munson,
  • Njagi Mwaniki,
  • Nasna Nassir,
  • Chiara Natali,
  • Shloka Negi,
  • Lingbin Ni,
  • Adam M. Novak,
  • Chie Owa,
  • Sadye Paez,
  • Benedict Paten,
  • Hiram Clawson,
  • Clelia Peano,
  • Adam M. Phillippy,
  • Brandon D. Pickett,
  • Laura Pignata,
  • Nadia Pisanti,
  • David Porubsky,
  • Pjotr Prins,
  • Anandi Radhakrishnan,
  • T. Rhyker Ranallo-Benavidez,
  • Brian J. Raney,
  • Mikko Rautiainen,
  • Alessandro Raveane,
  • Luyao Ren,
  • Arang Rhie,
  • Farnaz Salehi,
  • Samuel Sacco,
  • Michael C. Schatz,
  • Laura B. Scheinfeldt,
  • Aarushi Sehgal,
  • William E. Seligmann,
  • Mahsa Shabani,
  • Kishwar Shafin,
  • Shadi Shahatit,
  • Ruhollah Shemirani,
  • Vikram S. Shivakumar,
  • Swati Sinha,
  • Jouni Sirén,
  • Linnéa Smeds,
  • Steven J. Solar,
  • Marco Sollitto,
  • Nicole Soranzo,
  • Andrew B. Stergachis,
  • Marie-Marthe Suner,
  • Yoshihiko Suzuki,
  • Arda Söylev,
  • Jack AS Tierney,
  • Chad Tomlinson,
  • Francesca Floriana Tricomi,
  • Mohammed Uddin,
  • Matteo Tommaso Ungaro,
  • Rahul Varki,
  • Flavia Villani,
  • Mitchell R. Vollger,
  • Brian P. Walenz,
  • Charles Wang,
  • Lisa E. Wang,
  • Ting Wang,
  • Aaron M. Wenger,
  • Conor V. Whelan,
  • Zilan Xin,
  • Zheng Xu,
  • Kai Ye,
  • DongAhn Yoo,
  • Wenjin Zhang,
  • Ying Zhou,
  • Ivo Violich,
  • Giulia Zunino

摘要

Long-read RNA sequencing is a powerful technology to link transcript structures to genetic variants, but this type of analysis is not often performed owing to the lack of end-user tools. Here we introduce longcallR for joint single-nucleotide polymorphism calling, haplotype phasing and allele-specific analysis, which achieves high accuracy on benchmark datasets. Applied to 202 human samples, longcallR identified 88 significant allele-specific splicing events per sample on average, of which 46% involved unannotated junctions.