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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
..., none of which could be resolved upon manual inspection. These unconfirmed flagged errors represent either assembly errors too large for our reads, or artifacts owing to uneven read coverage or mapping.View this table: In this window In a new window Table 2. Flagger evaluation of draft and finished...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere assembly of C. elegans, generated from CGC1, an isogenic...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
.... 1987; Li et al. 2018), genomic imprinting (Li et al. 1993; Suzuki et al. 2007; Court et al. 2014), X-Chromosome inactivation (Sharp et al. 2011), and transcription repression (Moore et al. 2013). As a result, variations in DNA methylation have been associated with human diseases such as aging...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...there are not enough unikmers to resolve them. This observation is supported by Figure 3B, which illustrates that the number of unikmers decreases with P. However, the mutation rate in eukaryotic s is generally higher than one SNP over a 1000 bp (Risch 2000; International Human Genome Sequencing Consortium 2001; Orr...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...to classify s with the Genome Taxonomy Database. Bioinformatics 36: 1925–1927. doi:10.1093/bioinformatics/btz848 ↵Cheng H, Sun YH, Yang Q, Deng MG, Yu ZJ, Zhu G, Qu JX, Liu L, Yang L, Xia Y. 2022. A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
..., University of California San Diego, La Jolla, California 92093, USA; 3UC Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA Corresponding author: ppevzner@ucsd.eduAbstractThe advent of long and accurate “HiFi” reads has greatly improved our ability to generate complete meta-assembled s (MAGs...
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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
...for all scaffolds of A. castellanii strains C3 and Neff assemblies >50 kb.View this table: In this window In a new window Table 1. Genome statistics for the finished assemblies of Neff, C3 (this study), and the reference Neff-v1 Hi-C contact maps present a convenient readout to explore large misassemblies...
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Research: Human contamination in bacterial genomes has created thousands of spurious proteins
- Florian P. Breitwieser,
- Mihaela Pertea,
- Aleksey V. Zimin,
- and Steven L. Salzberg
Genome Res. June 2019 29: 954-960; Published in Advance May 7, 2019, doi:10.1101/gr.245373.118
...contributed substantially to the ongoing presence of human contamination in draft s.As an illustration, consider Figure 1, which shows the alignment of a whole- shotgun data set from one of the Simons Genome Diversity Project s (Mallick et al. 2016) to GRCh38. The region shown is near the centromere...
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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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