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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
...in the Integrative Genomics Viewer (IGV) (Robinson et al. 2017). If switch errors were detected, the Clair3 VCF was edited before running “whatshap split” with default parameters to produce hap1 and hap2 phased FASTQs. Lastly, de novo assembly was produced from the haplotype-separated reads using Flye (v 2...
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Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...the ones that are previously traversed and are thus discarded in the next iteration of the decoding algorithm.Since our methodology is optimized for haploid assembly, we evaluate GNNome on the homozygous human CHM13 (Nurk et al. 2022) derived from a hydatidiform mole, along with the inbred s of Mus...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
.... This was the case for a HiFi-based HiCanu assembly of the haploid human cell line CHM13, derived from a hydatidiform mole (Nurk et al. 2020). This assembly resolved nine of 23 expected centromeric regions. To assess the incorporation of centromeric regions in the rat assembly, we used StainedGlass software (Vollger...
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Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
- Brianna Chrisman,
- Chloe He,
- Jae-Yoon Jung,
- Nate Stockham,
- Kelley Paskov,
- Peter Washington,
- Juli Petereit,
- and Dennis P. Wall
Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
...spectrum of genetic diversity that exists in the human species. Because of this incompleteness, reads originating from heterochromatic regions of the or from alternative haplotypes not well represented on the reference are not analyzed in most genomic studies. On a population scale, we therefore understand...
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Perspective: Short arms of human acrocentric chromosomes and the completion of the human genome sequence
- Stylianos E. Antonarakis
Genome Res. April 2022 32: 599-607; Published in Advance March 31, 2022, doi:10.1101/gr.275350.121
...Genet 86: 375–382. doi:10.1007/BF00201838 ↵Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, Shiryev SA, Morgulis A, Surti U, Warren WC, et al. 2014. Single haplotype assembly of the human from a hydatidiform mole. Genome Res 24: 2066–2076. doi:10.1101/gr.180893...
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Commentary: Implications of the first complete human genome assembly Genome Res. April 2022 32: 595-598; Published in Advance March 31, 2022, doi:10.1101/gr.276723.122

...Implications of the first complete human assemblyThe Telomere-to-Telomere (T2T) Consortium has recently announced the assembly and analysis of the first complete human assembly. The use of the functionally haploid CHM13hTERT cell line (CHM13), originally isolated from a hydatidiform mole, as well...
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Research: Delayed DNA replication in haploid human embryonic stem cells
- Matthew M. Edwards,
- Michael V. Zuccaro,
- Ido Sagi,
- Qiliang Ding,
- Dan Vershkov,
- Nissim Benvenisty,
- Dieter Egli,
- and Amnon Koren
Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
.... Diploidization is not specific to parthenogenicity, as hydatidiform moles forming from the loss of the nucleus in a fertilized egg are found to be diploid as well (Fan et al. 2002). Similarly, most androgenetic stem cells derived from haploid eggs with only a paternal are also diploid (Sagi et al. 2019).It has...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
..., underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary assemblies. We generated highly contiguous de novo reference s for the Drosophila simulans species complex (D. simulans, D...
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Research: Discovery and genotyping of structural variation from long-read haploid genome sequence data
- John Huddleston,
- Mark J.P. Chaisson,
- Karyn Meltz Steinberg,
- Wes Warren,
- Kendra Hoekzema,
- David Gordon,
- Tina A. Graves-Lindsay,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Laura Vives,
- Paul Peluso,
- Matthew Boitano,
- Chen-Shin Chin,
- Jonas Korlach,
- Richard K. Wilson,
- and Evan E. Eichler
Genome Res. May 2017 27: 677-685; Published in Advance November 28, 2016, doi:10.1101/gr.214007.116
...(WGS) data derived from a hydatidiform mole, CHM1, and a second haploid human from a different hydatidiform mole, CHM13. The combination of these two haploid human s allowed us to identify and rapidly validate haplotype-specific SVs and indels. We used this to establish the baseline of variation we...
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Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- Ian T. Fiddes,
- Joel Armstrong,
- Mark Diekhans,
- Stefanie Nachtweide,
- Zev N. Kronenberg,
- Jason G. Underwood,
- David Gordon,
- Dent Earl,
- Thomas Keane,
- Evan E. Eichler,
- David Haussler,
- Mario Stanke,
- and Benedict Paten
Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
...al. 2016; Huddleston et al. 2017; Korlach et al. 2017) (Falcon) and 10x Genomics (Weisenfeld et al. 2017) (Supernova) provide tools to construct phased, diploid assemblies. Annotating diploid assemblies provides a window into haplotype-specific structural variation that may affect gene expression...

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