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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
...also examined two ONT assemblies generated with Flye (Kolmogorov et al. 2019), with different read length cutoffs (1 kb and 45 kb; the coverages are 400× and 100×). Briefly, we checked for each mRNA, the proportion of its sequence that is present in the assemblies (Supplemental Methods). The rationale...
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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
...exon 1 of the APC gene (Fig. 2D). RNA-seq analysis revealed a substantial decrease in APC expression in the tumor sample (tumor fragments per kilobase of transcript per million fragments mapped (FPKM): 0.296 vs. normal FPKM: 2.262). The SV was not detected by short-read sequencing, likely because...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...further investigated the impact of the HBV-induced TRA on the expression of genes situated on either side. Long-read RNA-seq was performed on both the HCC13_T1 tumor sample and its corresponding adjacent nontumor tissue. To obtain high-quality sequences, we conducted local assembly of the TRA using reads...
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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
..., expanding the applicability of long-read sequencing across diverse genomic studies (Wenger et al. 2019; Koren et al. 2024). Both platforms are capable of DNA and cDNA sequencing and detecting DNA methylation. At the same time, ONT offers additional functionalities such as adaptive sampling and direct RNA...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
.... 2020; Glinos et al. 2022; Veiga et al. 2022; Zhang et al. 2022), and represents a data source of great value for the de novo annotation of the Earth BioGenome Project (Lawniczak et al. 2022). Despite its strengths, LRS presents several shortcomings. The quality of long-read RNA sequencing (lrRNA...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...understanding of the evolutionary history and structural variation within these important chromosomes across large pan data sets such as the HPRC (Liao et al. 2023).To simplify sequencing requirements, Verkko2 now supports multiple long-read data types, in addition to HiFi, for initial construction of the LA...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...short-read sequences. Recent advances in long-read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single-cell samples. Here, we developed a new computational tool, CTAT-LR-Fusion, to detect fusion transcripts from long-read RNA-seq with or without...
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Resource: High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
- Zihe Li,
- Ziyu Xu,
- Lei Zhu,
- Tao Qin,
- Jinrui Ma,
- Zhanying Feng,
- Huishan Yue,
- Qing Guan,
- Botong Zhou,
- Ge Han,
- Guokun Zhang,
- Chunyi Li,
- Shuaijun Jia,
- Qiang Qiu,
- Dingjun Hao,
- Yong Wang,
- and Wen Wang
Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
....Based on the high-quality sika deer , we were able to integrate large amounts of omics data including bulk RNA-seq, single-cell RNA-seq, and ATAC-seq data, of sika deer to reconstruct the tissue-specific GRNs and resolve cellular dynamics during antler regeneration. The results reveal that antler PP shared some key...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...spicilegus and M. spretus) (geographical origins and evolutionary relationships are depicted in Fig. 2A). We performed both PacBio Iso-Seq and Illumina RNA-seq for each brain sample to generate high-quality transcriptomes. As a result, an average of 60.1 (standard deviation [SD]: 9.6) million raw subreads...
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Research: Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
- Maria Nattestad,
- Sara Goodwin,
- Karen Ng,
- Timour Baslan,
- Fritz J. Sedlazeck,
- Philipp Rescheneder,
- Tyler Garvin,
- Han Fang,
- James Gurtowski,
- Elizabeth Hutton,
- Elizabeth Tseng,
- Chen-Shan Chin,
- Timothy Beck,
- Yogi Sundaravadanam,
- Melissa Kramer,
- Eric Antoniou,
- John D. McPherson,
- James Hicks,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. August 2018 28: 1126-1135; Published in Advance June 28, 2018, doi:10.1101/gr.231100.117
...In addition to sequencing, we performed long-read transcriptome sequencing using PacBio Iso-Seq to capture full-length transcripts. Although traditional short-read RNA-seq approaches allow isoform quantification, in many cases these reads are too short to reconstruct all isoforms, even with paired...

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