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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
...variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...sequencing data (Supplemental Table S1). The resulting assembly was then used as input for the second HiRise scaffolding using Hi-C sequencing data (Fig. 1A; Supplemental Table S1).View larger version: In this window In a new window Figure 1. Genome assemblies. (A) Methodological workflow for the generation...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
.... For example, the 2009 identification of the mutation that causes SCA31 was achieved solely by “traditional” methods: bacterial artificial chromosome (BAC)-based cloning, Sanger sequencing, and Southern blot, with targeted shotgun resequencing (Sato et al. 2009).The techniques employed by the Human Genome...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...using Oxford Nanopore long reads. To account for the error-prone nature of long reads, we polished the first draft assemblies with paired-end shotgun Illumina sequences using HyPo (Kundu et al. 2019). The polished assemblies were then scaffolded with long-range Hi-C contacts using our probabilistic...
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Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
- Apurva Narechania,
- Dean Bobo,
- Kevin Deitz,
- Rob DeSalle,
- Paul J. Planet,
- and Barun Mathema
Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
...highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 s have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...representations of multiple species of the Xiphophorus genus. Compared with earlier assemblies based on short sequencing reads, all quality parameters are much improved (Table 1; Schartl et al. 2013; Shen et al. 2016). Xiphophorus models have been used as standard assemblies in comparing assembly statistics...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
...Comprehensive variation discovery and recovery of missing sequence in the pig using multiple de novo assemblies Mingzhou Li,1,9 Lei Chen,2,9 Shilin Tian,1,3,9 Yu Lin,3,9 Qianzi Tang,1,9 Xuming Zhou,4,9 Diyan Li,1 Carol K.L. Yeung,3 Tiandong Che,1 Long Jin,1 Yuhua Fu,1,5 Jideng Ma,1 Xun Wang,1 Anan...
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Method: TransRate: reference-free quality assessment of de novo transcriptome assemblies
- Richard Smith-Unna,
- Chris Boursnell,
- Rob Patro,
- Julian M. Hibberd,
- and Steven Kelly
Genome Res. August 2016 26: 1134-1144; Published in Advance June 1, 2016, doi:10.1101/gr.196469.115
....kelly@plants.ox.ac.uk Abstract TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors...
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Method: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
- Nicholas H. Putnam,
- Brendan L. O'Connell,
- Jonathan C. Stites,
- Brandon J. Rice,
- Marco Blanchette,
- Robert Calef,
- Christopher J. Troll,
- Andrew Fields,
- Paul D. Hartley,
- Charles W. Sugnet,
- David Haussler,
- Daniel S. Rokhsar,
- and Richard E. Green
Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
...://creativecommons.org/licenses/by/4.0/. Method 342 Genome Research 26:342–350 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/16; www..org www..org SequencingConsortium2004). In contrast, a recent comparison of the performance of whole- shotgun (WGS) assembly software pipelines, each run by their developers on very...
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Method: Direct determination of diploid genome sequences
- Neil I. Weisenfeld,
- Vijay Kumar,
- Preyas Shah,
- Deanna M. Church,
- and David B. Jaffe
Genome Res. May 2017 27: 757-767; Published in Advance April 5, 2017, doi:10.1101/gr.214874.116
...have been demonstrated for small and midsized s (Jones et al. 2004; Chin et al. 2016). There are two extant instances of diploid de novo assemblies of human s—one obtained by Sanger sequencing of multiple libraries (Levy et al. 2007), and one from thousands of separate clone pools, each representing...
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