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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
...for projects aiming to interpret and compare variants.View larger version: In this window In a new window Figure 2. Schematic workflow for long-read-based genomic analysis. The workflow outlines the two approaches to analyzing long-read sequencing data. It details the different routes a researcher can take...
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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
...Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge CB10 1SA, United Kingdom Corresponding author: ana.conesa@csic.esAbstractLong-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
.... 2018).An important resource underpinning both basic and applied research is the rice reference sequence, originally released with two draft assemblies circa 2002 (for indica and japonica) (Goff et al. 2002; Yu et al. 2002) and then with one finished 3 years later by the International Rice Genome...
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Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- Jonas A. Gustafson,
- Sophia B. Gibson,
- Nikhita Damaraju,
- Miranda P.G. Zalusky,
- Kendra Hoekzema,
- David Twesigomwe,
- Lei Yang,
- Anthony A. Snead,
- Phillip A. Richmond,
- Wouter De Coster,
- Nathan D. Olson,
- Andrea Guarracino,
- Qiuhui Li,
- Angela L. Miller,
- Joy Goffena,
- Zachary B. Anderson,
- Sophie H.R. Storz,
- Sydney A. Ward,
- Maisha Sinha,
- Claudia Gonzaga-Jauregui,
- Wayne E. Clarke,
- Anna O. Basile,
- André Corvelo,
- Catherine Reeves,
- Adrienne Helland,
- Rajeeva Lochan Musunuri,
- Mahler Revsine,
- Karynne E. Patterson,
- Cate R. Paschal,
- Christina Zakarian,
- Sara Goodwin,
- Tanner D. Jensen,
- Esther Robb,
- The 1000 Genomes ONT Sequencing Consortium,
- University of Washington Center for Rare Disease Research (UW-CRDR),
- Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
- William Richard McCombie,
- Fritz J. Sedlazeck,
- Justin M. Zook,
- Stephen B. Montgomery,
- Erik Garrison,
- Mikhail Kolmogorov,
- Michael C. Schatz,
- Richard N. McLaughlin, Jr.,
- Harriet Dashnow,
- Michael C. Zody,
- Matt Loose,
- Miten Jain,
- Evan E. Eichler,
- and Danny E. Miller
Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
...diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control data sets for variant filtering and prioritization has made tertiary analysis of LRS...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
.... 2020; Jiao et al. 2025). These interactions often fuel hybrid genomic conflicts. Short-read sequencing technologies have struggled to resolve such complexities owing to inherent limitations in assembly. In contrast, the advent of long-read sequencing technologies, such as of Pacific Biosciences (Pac...
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Methods: De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
- Josephine A. Reinhardt,
- David A. Baltrus,
- Marc T. Nishimura,
- William R. Jeck,
- Corbin D. Jones,
- and Jeffery L. Dangl
Genome Res. February 2009 19: 294-305; Published in Advance November 17, 2008, doi:10.1101/gr.083311.108
...and Arabidopsis pathogen, Pto DC3000 , facilitated development and testing of our method. Sequencing of a distantly related rice pathogen, Por 1_ 6 , demonstrated our method's efficacy for de novo assembly of novel genomes. Our assembly of Por 1_6 yielded an N50 scaffold size of 531,821 bp with &gt;75...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...to a single reference (Quadrana et al. 2016; Carpentier et al. 2019; Domínguez et al. 2020; Wyler et al. 2020; Qiu et al. 2021). With continued advancements in long-read sequencing technologies and improved assembly algorithms, there is a growing movement in genomics toward pangenomic-based approaches (Bayer...
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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
..., DeepTrio (DT) uses separate parental and offspring checkpoints to identify variants in related duo or trio samples (Kolesnikov et al. 2021). Furthermore, the haplotype-aware PEPPER–Margin–DV pipeline is a common approach for small variant detection with PacBio's long-read sequencing (Shafin et al. 2021...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
.... Here, we construct a graph pan from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white-head-associated locus for the first time based on long-read sequencing data and pan analyses. We introduce a pan-wide association mapping approach that examines...
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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
..., Munson KM, Hoekzema K, Porubsky D, Beck CR, Marschall T, Garimella K, et al. 2023. Whole- long-read sequencing downsampling and its effect on variant-calling precision and recall. Genome Res 33: 2029–2040. doi:10.1101/gr.278070.123 ↵Jansen S, Aigner B, Pausch H, Wysocki M, Eck S, Benet-Pagès A, Graf E...

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