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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
...Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere assembly, phasing, and scaffolding Dmitry Antipov1,4, Mikko Rautiainen2,4, Sergey Nurk3, Brian P. Walenz1, Steven J. Solar1, Adam M. Phillippy1 and Sergey Koren1 1Genome Informatics Section...
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Method: HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay
- Jia Lv,
- Wenqian Jiao,
- Haobing Guo,
- Pingping Liu,
- Ruijia Wang,
- Lingling Zhang,
- Qifan Zeng,
- Xiaoli Hu,
- Zhenmin Bao,
- and Shi Wang
Genome Res. December 2018 28: 1919-1930; Published in Advance November 8, 2018, doi:10.1101/gr.235820.118
...for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called HD-Marker), which addresses the array-related issues of original GoldenGate methodology and allows for highly multiplexed and flexible targeted genotyping of more than 12,000 loci...
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Method: Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
- Nadin Rohland and
- David Reich
Genome Res. May 2012 22: 939-946; Published in Advance January 20, 2012, doi:10.1101/gr.128124.111
..., such as the Illumina TruSeq Enrichment kits (Clark et al. 2011), the Roche/NimbleGen SeqCap EZ Hybridization kits, and array-based hybridization (Hodges et al. 2007), would enrich multiplexed samples as efficiently as the Agilent system if the libraries are prepared with short adapters. There are several potential...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...populations. The discovery of distinct genotypes may further reveal associations with pharmacology, drug response, or metabolism. We note here that the population-wide analysis of genetic diversity of long-tailed macaques on Mauritius offers the unique opportunity to study the rapid expansion of an isolated...
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Method: Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
- Jamie K. Teer,
- Lori L. Bonnycastle,
- Peter S. Chines,
- Nancy F. Hansen,
- Natsuyo Aoyama,
- Amy J. Swift,
- Hatice Ozel Abaan,
- Thomas J. Albert,
- NISC Comparative Sequencing Program,
- Elliott H. Margulies,
- Eric D. Green,
- Francis S. Collins,
- James C. Mullikin,
- and Leslie G. Biesecker
Genome Res. October 2010 20: 1420-1431; Published in Advance September 1, 2010, doi:10.1101/gr.106716.110
...), and 91% (MGS) for 400 Mb. In contrast, all methods yielded similar accuracies of &gt;99.84% when compared to Infinium 1M SNP BeadChip-derived genotypes and &gt;99.998% when compared to 30-fold coverage whole-genome shotgun sequencing data. We also observed a low false-positive rate with all three methods...
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Method: Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
- Jeffrey S. McLean,
- Mary-Jane Lombardo,
- Michael G. Ziegler,
- Mark Novotny,
- Joyclyn Yee-Greenbaum,
- Jonathan H. Badger,
- Glenn Tesler,
- Sergey Nurk,
- Valery Lesin,
- Daniel Brami,
- Adam P. Hall,
- Anna Edlund,
- Lisa Z. Allen,
- Scott Durkin,
- Sharon Reed,
- Francesca Torriani,
- Kenneth H. Nealson,
- Pavel A. Pevzner,
- Robert Friedman,
- J. Craig Venter,
- and Roger S. Lasken
Genome Res. May 2013 23: 867-877; Published in Advance April 5, 2013, doi:10.1101/gr.150433.112
..., culturing will yield only a fraction of the species present, PCR of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect strain variations. In this study, we present a single-cell genome sequencing approach to address...
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Methods: Mapping translocation breakpoints by next-generation sequencing
- Wei Chen,
- Vera Kalscheuer,
- Andreas Tzschach,
- Corinna Menzel,
- Reinhard Ullmann,
- Marcel Holger Schulz,
- Fikret Erdogan,
- Na Li,
- Zofia Kijas,
- Ger Arkesteijn,
- Isidora Lopez Pajares,
- Margret Goetz-Sothmann,
- Uwe Heinrich,
- Imma Rost,
- Andreas Dufke,
- Ute Grasshoff,
- Birgitta Glaeser,
- Martin Vingron,
- and H. Hilger Ropers
Genome Res. July 2008 18: 1143-1149; Published in Advance March 7, 2008, doi:10.1101/gr.076166.108
...of BAC-FISH is often insufficient to unequivocally identify the disrupted gene. To overcome these limitations, we have performed shotgun sequencing of flow-sorted derivative chromosomes using “next-generation” (Illumina/Solexa) multiplex sequencing-by-synthesis technology. As shown here for three...
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Method: A reduced representation approach to population genetic analyses and applications to human evolution
- Francesca Luca,
- Richard R. Hudson,
- David B. Witonsky,
- and Anna Di Rienzo
Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110
...reduced representation protocols aimed to develop markers for subsequent genotyping studies and did not attempt to estimate evolutionary parameters. In general, obtaining unbiased estimates of evolutionary parameters based on shotgun sequence data presents several challenges, which include sequencing...
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Next-Generation DNA Sequencing/Review: The new paradigm of flow cell sequencing
- Robert A. Holt and
- Steven J.M. Jones
Genome Res. June 2008 18: 839-846; doi:10.1101/gr.073262.107
...The new paradigm of flow cell sequencing Robert A. Holt 1 and Steven J.M. Jones British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada Abstract DNA sequencing is in a period of rapid change, in which...
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Chicken Special/Resources: Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates
- Wendy A. Kellner,
- Robert T. Sullivan,
- Brian H. Carlson,
- and James W. Thomas
Genome Res. January 2005 15: 166-173; Published in Advance December 8, 2004, doi:10.1101/gr.3066805
...more vertebrates in the near future, targeted comparative mapping and sequencing is an efficient, rapid, and complementary approach for addressing directed biological questions in an even greater breadth of species ( Gottgens et al. 2000 ; Chiu et al. 2002 , 2004 ; Thomas et al. 2003 ). In addition...

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