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Journal articles on the topic 'Haplotype assembly'

Author: Grafiati

Published: 9 March 2023

Last updated: 19 July 2025

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1

Owens, John Benjamin (Ben), Wolfgang Wüster, John Mulley, Stuart Graham, Rhys Morgan, and Axel Barlow. "The genome sequence of the common adder, Vipera berus (Linnaeus, 1758)." Wellcome Open Research 10 (January 14, 2025): 11. https://doi.org/10.12688/wellcomeopenres.23470.1.

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We present a genome assembly from an individual female Vipera berus (common adder; Chordata; Lepidosauria; Squamata; Viperidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,695.0 megabases and 1,476.7 megabases, respectively. Most of haplotype 1 (98.45%) is scaffolded into 19 chromosomal pseudomolecules, while haplotype 2 is assembled to scaffold level. The mitochondrial genome has also been assembled and is 17.35 kilobases in length.

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2

Izquierdo Arànega, Guillem, Joan Ferrer Obiol, Raül Ramos Garcia, Marta Riutort León, Julio Rozas Liras, and Jacob González-Solís Bou. "The genome sequence of Cory’s shearwater, Calonectris borealis (Cory, 1881)." Wellcome Open Research 9 (November 12, 2024): 678. http://dx.doi.org/10.12688/wellcomeopenres.23354.1.

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We present a genome assembly from an individual female Calonectris borealis (Cory’s shearwater; Chordata; Aves; Procellariiformes; Procellariidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,366.19 megabases and 1,211.47 megabases, respectively. Most of the assembly for haplotype 1 is scaffolded into 41 chromosomal pseudomolecules, including the Z and W sex chromosomes. Haplotype 2 has 39 autosomes. The mitochondrial genome has also been assembled and is 19.95 kilobases in length.

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3

Wang, Jiayi. "Research Status of Haplotype Assembly Technology." International Journal of Computer Science and Information Technology 2, no. 1 (2024): 466–75. http://dx.doi.org/10.62051/ijcsit.v2n1.49.

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Haplotype, also called haploid genotype, refers to the combination of a series of variant loci located on the same chromosome. Most of the current assembly algorithms ignore the heterozygous SNP variant sites on the chromosome and assemble a pseudohaplotype sequence. Due to the importance of haplotypes for the treatment of diseases, the mining of pathogenic genes and other medical organisms, haplotype analysis methods have become particularly important. At present, the indirect haplotype inference technology mainly includes two types: the alignment-based haplotyping algorithm and the assembly-

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4

Lopez Colom, Rosa, and Michelle O’Brien. "The genome sequence of the red fox, Vulpes vulpes (Linnaeus, 1758)." Wellcome Open Research 10 (January 14, 2025): 13. https://doi.org/10.12688/wellcomeopenres.23516.1.

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We present a genome assembly from an individual female Vulpes vulpes (red fox; Chordata, Mammalia, Carnivora, Canidae). The assembly comprises two haplotypes, with total lengths of 2,411.71 megabases and 2,398.53 megabases, respectively. For both haplotypes, 97.8% of haplotype 1 and 97.97% of haplotype 2 are scaffolded into 17 chromosomal pseudomolecules. Additionally, the mitochondrial genome has been assembled, with a total length of 16.68 kilobases.

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5

Adkins, Patrick, John Bishop, Joanna Harley, and Peter W. H. Holland. "The genome sequence of the amphioxus, Branchiostoma lanceolatum (Pallas, 1774)." Wellcome Open Research 10 (February 24, 2025): 95. https://doi.org/10.12688/wellcomeopenres.23671.1.

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We present a genome assembly from a specimen of Branchiostoma lanceolatum (Amphioxus; Chordata; Leptocardii; Amphioxiformes; Branchiostomatidae). The assembly contains two haplotypes with total lengths of 468.40 megabases and 465.81 megabases, respectively. Most of haplotype 1 (99.34%) is scaffolded into 19 chromosomal pseudomolecules. Haplotype 2 is a scaffold level assembly. The mitochondrial genome has also been assembled and is 15.14 kilobases in length.

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6

Feiner, Nathalie, Tobias Uller, Daniele Salvi, and Joana Meier. "The genome sequence of the Italian wall lizard, Podarcis siculus (Rafinesque-Schmaltz, 1810)." Wellcome Open Research 10 (May 20, 2025): 255. https://doi.org/10.12688/wellcomeopenres.24167.1.

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We present a genome assembly from a female specimen of Podarcis siculus (Italian wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,571.36 megabases and 1,455.93 megabases. Most (95.7%) of the haplotype 1 assembly is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.15 kilobases.

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7

Canizales-Silva, Cristian, Mateo A. Alvarado-Lopez, Carolina Hernández, et al. "The genome sequence of the kissing bug, Panstrongylus geniculatus (Latreille, 1811)." Wellcome Open Research 10 (February 3, 2025): 43. https://doi.org/10.12688/wellcomeopenres.23631.1.

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We present a genome assembly from an individual female Panstrongylus geniculatus (kissing bug; Arthropoda; Insecta; Hemiptera; Reduviidae). The assembly contains two haplotypes with total lengths of 1,362.73 megabases and 1,342.40 megabases, respectively. Most of haplotype 1 (97.5%) is scaffolded into 12 chromosomal pseudomolecules. Haplotype 2 is assembled to scaffold level. The mitochondrial genome has also been assembled and is 17.44 kilobases in length.

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8

Falk, Steven, Liam M. Crowley, and Olga Sivell. "The genome sequence of a cluster fly, Pollenia pediculata Macquart, 1834." Wellcome Open Research 10 (April 11, 2025): 190. https://doi.org/10.12688/wellcomeopenres.23961.1.

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We present a genome assembly from a female specimen of Pollenia pediculata (cluster fly; Arthropoda; Insecta; Diptera; Polleniidae). The assembly contains two haplotypes with total lengths of 1,156.86 megabases and 1,222.48 megabases. Most of haplotype 1 (99.79%) is scaffolded into 6 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.82 kilobases.

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9

Falk, Steven, and Liam M. Crowley. "The genome sequence of the tephritid fly, Campiglossa producta (Loew, 1844)." Wellcome Open Research 10 (June 2, 2025): 286. https://doi.org/10.12688/wellcomeopenres.24327.1.

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We present a genome assembly from a female specimen of Campiglossa producta (tephritid fly; Arthropoda; Insecta; Diptera; Tephritidae). The assembly contains two haplotypes with total lengths of 865.96 megabases and 843.00 megabases. Most of haplotype 1 (96.26%) is scaffolded into 6 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.79 kilobases.

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Edgecombe, Gregory D., Liam M. Crowley, Mark G. Telfer, and Lauren Hughes. "The genome sequence of the banded centipede, Lithobius variegatus Leach, 1814." Wellcome Open Research 10 (June 2, 2025): 285. https://doi.org/10.12688/wellcomeopenres.24329.1.

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We present a genome assembly from a female specimen of Lithobius variegatus (banded centipede; Arthropoda; Chilopoda; Lithobiomorpha; Lithobiidae). The assembly contains two haplotypes with total lengths of 1,766.49 megabases and 1,768.00 megabases. Most of haplotype 1 (97.68%) is scaffolded into 23 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.44 kilobases.

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11

Sivell, Duncan, Dmitry Telnov, Michael F. Geiser, and Maxwell V. L. Barclay. "The genome sequence of the click beetle, Ampedus sanguinolentus sanguinolentus (Schrank, 1776)." Wellcome Open Research 10 (February 24, 2025): 96. https://doi.org/10.12688/wellcomeopenres.23712.1.

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We present a genome assembly from a female specimen of Ampedus sanguinolentus sanguinolentus (click beetle; Arthropoda; Insecta; Coleoptera; Elateridae). The assembly contains two haplotypes with total lengths of 1,574.76 megabases and 1,572.87 megabases. Most of haplotype 1 (97.13%) is scaffolded into 10 chromosomal pseudomolecules, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 15.99 kilobases in length.

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12

Hunter, Tony. "The genome sequence of the tawny cockroach, Ectobius (Ectobius) pallidus (Olivier, 1789)." Wellcome Open Research 10 (January 15, 2025): 22. https://doi.org/10.12688/wellcomeopenres.23463.1.

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We present a genome assembly from a specimen of Ectobius pallidus (tawny cockroach; Arthropoda; Insecta; Blattodea; Ectobiidae). The assembly contains two haplotypes with total lengths of 2,087.55 megabases and 2,124.67 megabases, respectively. Most of haplotype 1 (98.55%) is scaffolded into 11 chromosomal pseudomolecules, while haplotype 2 is assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.75 kilobases in length.

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13

Boyes, Douglas, and Clare Boyes. "The genome sequence of the Alder Moth, Acronicta alni (Linnaeus, 1767)." Wellcome Open Research 10 (February 12, 2025): 68. https://doi.org/10.12688/wellcomeopenres.23704.1.

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We present a genome assembly from a male Acronicta alni (Alder Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 470.37 megabases and 472.86 megabases. Most of haplotype 1 (98.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.

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14

Pearce, Nicola, Michelle F. O’Brien, and Rosa Lopez Colom. "The genome sequence of the European mole, Talpa europaea Linnaeus, 1758." Wellcome Open Research 10 (February 24, 2025): 98. https://doi.org/10.12688/wellcomeopenres.23759.1.

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We present a genome assembly from a female Talpa europaea (European mole; Chordata; Mammalia; Eulipotyphla; Talpidae). The assembly contains two haplotypes with total lengths of 2,060.98 megabases and 2,056.47 megabases. Most of haplotype 1 (98.6%) is scaffolded into 17 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 16.93 kilobases in length.

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15

Wolton, Robert. "The genome sequence of the Slender-footed Robberfly, Leptarthrus brevirostris (Meigen, 1804)." Wellcome Open Research 10 (May 23, 2025): 273. https://doi.org/10.12688/wellcomeopenres.24277.1.

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We present a genome assembly from a female specimen of Leptarthrus brevirostris (Slender-footed Robberfly; Arthropoda; Insecta; Diptera; Asilidae). The assembly contains two haplotypes with total lengths of 850.81 megabases and 851.46 megabases. Most of haplotype 1 (99.05%) is scaffolded into 6 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 18.16 kilobases.

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16

Crowley, Liam M., and Xavier Richard Badham. "The genome sequence of a fungus weevil, Platystomos albinus (C.Linnaeus, 1758)." Wellcome Open Research 10 (June 2, 2025): 295. https://doi.org/10.12688/wellcomeopenres.24290.1.

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We present a genome assembly from a female specimen of Platystomos albinus (fungus weevil; Arthropoda; Insecta; Coleoptera; Anthribidae). The assembly contains two haplotypes with total lengths of 555.31 megabases and 554.55 megabases. Haplotype 1 is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.09 kilobases.

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17

Walsh, Grace, Barry O’ Donoghue, Jacob Höglund, and Barry John McMahon. "The genome sequence of the Eurasian Curlew, Numenius arquata (Linnaeus, 1758)." Wellcome Open Research 10 (June 2, 2025): 298. https://doi.org/10.12688/wellcomeopenres.24272.1.

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We present a genome assembly from a female specimen of Numenius arquata (Eurasian Curlew; Chordata; Aves; Charadriiformes; Scolopacidae). The assembly contains two haplotypes with total lengths of 1,348.86 megabases and 1,198.36 megabases. Most of haplotype 1 (89.99%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.13 kilobases. Gene annotation of this assembly on Ensembl identified 15,412 protein-coding genes.

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18

Willink, Beatriz. "The genome sequence of the Tropical Bluetail Damselfly, Ischnura senegalensis (Rambur, 1842)." Wellcome Open Research 10 (February 24, 2025): 104. https://doi.org/10.12688/wellcomeopenres.23747.1.

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We present a genome assembly from a specimen of Ischnura senegalensis (Tropical Bluetail; Arthropoda; Insecta; Odonata; Coenagrionidae). The assembly contains two haplotypes with total lengths of 1,599.82 megabases and 1,602.78 megabases. Most of haplotype 1 (96.41%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome, which haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 18.11 kilobases in length.

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19

Humby, Toby D., Michelle O'Brien, and Rosa Lopez Colom. "The genome sequence of the mallard, Anas platyrhynchos Linnaeus, 1758." Wellcome Open Research 10 (February 24, 2025): 94. https://doi.org/10.12688/wellcomeopenres.23744.1.

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We present a genome assembly from an individual female Anas platyrhynchos (Mallard; Chordata; Aves; Anseriformes; Anatidae). The assembly contains two haplotypes with total lengths of 1,300.23 megabases and 1,136.57 megabases, respectively. Most of haplotype 1 (91.77%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z chromosomes, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 16.61 kilobases in length.

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20

Barclay, Maxwell V. L., Svetlana Nikolaeva, and Dmitry Telnov. "The genome sequence of the false flower beetle, Anaspis frontalis (Linnaeus, 1758)." Wellcome Open Research 10 (February 19, 2025): 82. https://doi.org/10.12688/wellcomeopenres.23726.1.

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We present a genome assembly from a specimen of Anaspis frontalis (the false flower beetle; Arthropoda; Insecta; Coleoptera; Scraptiidae). The assembly contains two haplotypes with total lengths of 808.55 megabases and 802.05 megabases. Most of haplotype 1 (95.81%) is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.

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21

Blows, Elizabeth. "The genome sequence of the Common Buzzard, Buteo buteo (Linnaeus, 1758)." Wellcome Open Research 10 (March 14, 2025): 130. https://doi.org/10.12688/wellcomeopenres.23873.1.

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We present a genome assembly from a male specimen of Buteo buteo (Common Buzzard; Chordata; Aves; Accipitriformes; Accipitridae). The assembly contains two haplotypes with total lengths of 1,303.68 megabases and 1,330.55 megabases. Most of haplotype 1 (94.6%) is scaffolded into 34 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled, with a length of 18.36 kilobases.

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Feiner, Nathalie, Tobias Uller, Javier Abalos, and Joana Meier. "The genome sequence of the Maltese wall lizard, Podarcis filfolensis (Bedriaga, 1876)." Wellcome Open Research 10 (April 23, 2025): 213. https://doi.org/10.12688/wellcomeopenres.24042.1.

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We present a genome assembly from a female specimen of Podarcis filfolensis (Maltese wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,506.95 megabases and 1,404.02 megabases. Most of haplotype 1 (98.73%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.23 kilobases.

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Feiner, Nathalie, Tobias Uller, Kinsey M. Brock, Panayiotis Pafilis, and Joana Meier. "The genome sequence of Erhard’s wall lizard, Podarcis erhardii (Bedriaga, 1882)." Wellcome Open Research 10 (April 23, 2025): 212. https://doi.org/10.12688/wellcomeopenres.24041.1.

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We present a genome assembly from a female specimen of Podarcis erhardii (Erhard's wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,495.98 megabases and 1,477.75 megabases. Most of haplotype 1 (99.28%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.14 kilobases.

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Boyes, Douglas, and Clare Boyes. "The genome sequence of the Feathered Thorn moth, Colotois pennaria (Linnaeus, 1761)." Wellcome Open Research 10 (April 30, 2025): 230. https://doi.org/10.12688/wellcomeopenres.23992.1.

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We present a genome assembly from a male specimen of Colotois pennaria (Feathered Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The assembly contains two haplotypes with total lengths of 449.44 megabases and 449.26 megabases. Most of haplotype 1 (99.91%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.57 kilobases.

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O’Brien, Michelle F., and Rosa Lopez Colom. "The genome sequence of the common crane, Grus grus (Linnaeus, 1758)." Wellcome Open Research 10 (March 4, 2025): 119. https://doi.org/10.12688/wellcomeopenres.23797.1.

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We present a genome assembly from a male specimen of Grus grus (common crane; Chordata; Aves; Gruiformes; Gruidae). The assembly contains two haplotypes with total lengths of 1,352.26 megabases and 1,291.08 megabases. Most of haplotype 1 (91.85%) is scaffolded into 40 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 18.9 kilobases in length.

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Boyes, Clare, and John P. Martin. "The genome sequence of the Sandhill Knot-horn moth, Anerastia lotella Hübner, 1813." Wellcome Open Research 10 (March 19, 2025): 148. https://doi.org/10.12688/wellcomeopenres.23898.1.

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We present a genome assembly from a female specimen of Anerastia lotella (Sandhill Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The assembly contains two haplotypes with total lengths of 1,079.72 megabases and 957.24 megabases. Most of haplotype 1 (99.38%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.31 kilobases.

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O’Brien, Michelle F., and Rosa Lopez Colom. "The genome sequence of the Common Pochard, Aythya ferina (Linnaeus, 1758)." Wellcome Open Research 10 (March 19, 2025): 152. https://doi.org/10.12688/wellcomeopenres.23904.1.

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We present a genome assembly from a female specimen of Aythya ferina (Common Pochard; Chordata; Aves; Anseriformes; Anatidae). The assembly contains two haplotypes with total lengths of 1,252.30 megabases and 1,103.59 megabases. Most of haplotype 1 (92.13%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.6 kilobases.

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Oxford, Geoff S. "The genome sequence of the Tansy Beetle, Chrysolina graminis (Linnaeus, 1758)." Wellcome Open Research 10 (June 2, 2025): 296. https://doi.org/10.12688/wellcomeopenres.24287.1.

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We present a genome assembly from a female specimen of Chrysolina graminis (Tansy Beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The assembly contains two haplotypes with total lengths of 1,467.20 megabases and 1,455.42 megabases. Most of haplotype 1 (98.03%) is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.07 kilobases.

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Christenhusz, Maarten J. M., Sahr Mian, Ilia J. Leitch, and Andrew R. Leitch. "The genome sequence of French Tamarisk, Tamarix gallica L." Wellcome Open Research 10 (April 25, 2025): 220. https://doi.org/10.12688/wellcomeopenres.24043.1.

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We present a genome assembly from a specimen of Tamarix gallica (Tamarisk; Streptophyta; Magnoliopsida; Caryophyllales; Tamaricaceae). The assembly contains two haplotypes with total lengths of 1,404.82 megabases and 1,536.15 megabases. Most of haplotype 1 (98.66%) is scaffolded into 12 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial and plastid genome assemblies have lengths of 483.72 kilobases and 156.16 kilobases, respectively.

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O’Brien, Michelle F., and Rosa Lopez Colom. "The genome sequence of the American mink, Neogale vison (Schreber, 1777)." Wellcome Open Research 10 (February 24, 2025): 103. https://doi.org/10.12688/wellcomeopenres.23780.1.

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We present a genome assembly from a female specimen of the American mink, Neogale vison (Chordata; Mammalia; Carnivora; Mustelidae). The assembly comprises two haplotypes, with total lengths of 2,697.13 megabases and 2,662.78 megabases, respectively. Most of haplotype 1 (98.72%) and haplotype 2 (98.73%) is scaffolded into 15 chromosomal pseudomolecules, including the X chromosome. The mitochondrial genome has also been assembled, with a length of 16.59 kilobases.

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Crowley, Liam M. "The genome sequence of the Bronze Shieldbug, Troilus luridus (Fabricius, 1775)." Wellcome Open Research 10 (May 20, 2025): 259. https://doi.org/10.12688/wellcomeopenres.24260.1.

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We present a genome assembly from a male specimen of Troilus luridus (Bronze Shieldbug; Arthropoda; Insecta; Hemiptera; Pentatomidae). The assembly contains two haplotypes with total lengths of 1,044.50 megabases and 842.58 megabases. Most of haplotype 1 (93.48%) is scaffolded into 8 chromosomal pseudomolecules, including the X and Y sex chromosomes. Most of haplotype 2 (93.27%) is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.9 kilobases.

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Feiner, Nathalie, Tobias Uller, Javier Abalos, Tahar Slimani, Abderrrahim S’Khifa, and Joana Meier. "The genome sequence of the Andalusian wall lizard, Podarcis vaucheri (Boulenger, 1905)." Wellcome Open Research 10 (May 20, 2025): 265. https://doi.org/10.12688/wellcomeopenres.24168.1.

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We present a genome assembly from a female specimen of Podarcis vaucheri (Andalusian wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,614.91 megabases and 1,510.74 megabases. Most of haplotype 1 (98.26%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Most of haplotype 2 (98.63%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.24 kilobases.

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Humby, Toby D., Michelle F. O’Brien, and Rosa Lopez Colom. "The genome sequence of the Eurasian Collared-Dove, Streptopelia decaocto (Frivaldszky, 1838)." Wellcome Open Research 10 (March 19, 2025): 150. https://doi.org/10.12688/wellcomeopenres.23900.1.

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We present a genome assembly from a male specimen of Streptopelia decaocto (Eurasian Collared-Dove; Chordata; Aves; Columbiformes; Columbidae). The assembly contains two haplotypes with total lengths of 1,290.94 megabases and 1,200.50 megabases. Most of haplotype 1 (86.6%) is scaffolded into 33 chromosomal pseudomolecules, including the Z sex chromosome. Most of haplotype 2 (92.76%) is scaffolded into 32 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.62 kilobases in length.

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Crowley, Liam M., and Denise C. Wawman. "The genome sequence of the Ruddy Darter, Sympetrum sanguineum (Müller, 1764)." Wellcome Open Research 10 (January 15, 2025): 23. https://doi.org/10.12688/wellcomeopenres.23466.1.

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We present a genome assembly from a male specimen of Sympetrum sanguineum (Ruddy Darter; Arthropoda; Insecta; Odonata; Libellulidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,500.53 megabases and 1,304.05 megabases. Most of haplotype 1 is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome, while haplotype 2 is scaffolded into 12 autosomes.

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Xu, Mengyang, Lidong Guo, Xiao Du, et al. "Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios." Bioinformatics 37, no. 15 (2021): 2095–102. http://dx.doi.org/10.1093/bioinformatics/btab068.

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Abstract Motivation Achieving a near complete understanding of how the genome of an individual affects the phenotypes of that individual requires deciphering the order of variations along homologous chromosomes in species with diploid genomes. However, true diploid assembly of long-range haplotypes remains challenging. Results To address this, we have developed Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy, or HAST, which uses parental information to classify reads into maternal or paternal. Once sorted, these reads are used to independently de novo assembl

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Ranallo-Benavidez, T. Rhyker, Yue Hao, Noelle Fukushima, Ogechukwu Mbegbu, and Floris P. Barthel. "EPCO-45. COMPLETE CHROMOSOME-SCALE DIPLOID-PHASED ASSEMBLY OF A NORMAL HUMAN ASTROCYTE CELL LINE." Neuro-Oncology 26, Supplement_8 (2024): viii12. http://dx.doi.org/10.1093/neuonc/noae165.0044.

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Abstract Genomic studies of the malignant brain tumor glioma invariably rely on aligning sequencing reads to a reference genome such as HG38, even though no single reference can capture the diversity of an individual patient or cell line. To begin addressing these biases in genomics research, we sought to construct a chromosome-scale diploid-phased assembly of a normal human astrocyte (NHA) cell line that is frequently used as a basis for developing isogenic glioma cell models. To achieve this, we generated 45x Pacific Biosciences HiFi data (N50: 16kb), 26x Oxford Nanopore Technologies ultra-l

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Coleman, Max, and Markus Ruhsam. "The genome sequence of wych elm, Ulmus glabra Huds." Wellcome Open Research 9 (December 3, 2024): 708. https://doi.org/10.12688/wellcomeopenres.23428.1.

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We present a genome assembly from a diploid specimen of Ulmus glabra (wych elm; Streptophyta; Magnoliopsida; Rosales; Ulmaceae). The assembly contains two haplotypes with total lengths of 1,788.20 megabases and 1,860.20 megabases, respectively. Most of haplotype 1 (97.9%) is scaffolded into 14 chromosomal pseudomolecules. Haplotype 2 was submitted as a scaffold-level assembly. The mitochondrial and plastid genome assemblies have lengths of 520.46 kilobases and 159.28 kilobases, respectively.

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Siragusa, Enrico, Niina Haiminen, Richard Finkers, Richard Visser, and Laxmi Parida. "Haplotype assembly of autotetraploid potato using integer linear programing." Bioinformatics 35, no. 18 (2019): 3279–86. http://dx.doi.org/10.1093/bioinformatics/btz060.

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Abstract Summary Haplotype assembly of polyploids is an open issue in plant genomics. Recent experimental studies on highly heterozygous autotetraploid potato have shown that available methods do not deliver satisfying results in practice. We propose an optimal method to assemble haplotypes of highly heterozygous polyploids from Illumina short-sequencing reads. Our method is based on a generalization of the existing minimum fragment removal model to the polyploid case and on new integer linear programs to reconstruct optimal haplotypes. We validate our methods experimentally by means of a comb

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Bahcall, Orli. "Single-haplotype genome assembly." Nature Genetics 46, no. 12 (2014): 1257. http://dx.doi.org/10.1038/ng.3157.

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Che, Tiandong, Jing Li, Xiaobo Li, et al. "Haplotype-resolved assembly of the mule duck genome using high-fidelity sequencing technology." PLOS ONE 19, no. 7 (2024): e0305914. http://dx.doi.org/10.1371/journal.pone.0305914.

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Mule duck is vitally important to the production of global duck meat. Here, we present two high-quality haplotypes of a female mule duck (haplotype 1 (H1):1.28 Gb, haplotype 2 (H2): 1.40 Gb). The continuity (H1: contig N50 = 14.90 Mb, H2: contig N50 = 15.70 Mb) and completeness (BUSCO: H1 = 96.9%, H2 = 97.3%) are substantially better than those of other duck genomes. We detected the structural variations (SVs) in H1 and H2. We observed a positive correlation between autosome length and the number of SVs. Z chromosome was some deficient in deletions and insertions, but W chromosome was some exc

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Rodriguez, Oscar L., Anna Ritz, Andrew J. Sharp, and Ali Bashir. "MsPAC: a tool for haplotype-phased structural variant detection." Bioinformatics 36, no. 3 (2019): 922–24. http://dx.doi.org/10.1093/bioinformatics/btz618.

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Abstract Summary While next-generation sequencing (NGS) has dramatically increased the availability of genomic data, phased genome assembly and structural variant (SV) analyses are limited by NGS read lengths. Long-read sequencing from Pacific Biosciences and NGS barcoding from 10x Genomics hold the potential for far more comprehensive views of individual genomes. Here, we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software) and convert assemblies into high-quality, phased SV predictions. MsPAC represents a framework for haplotyp

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Sun, Hequan, Wen-Biao Jiao, Kristin Krause, et al. "Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar." Nature Genetics 54, no. 3 (2022): 342–48. http://dx.doi.org/10.1038/s41588-022-01015-0.

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AbstractPotato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% we

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Abu-Bakar, Muhammad Abdullah, Monowar Hossain Md., and Chandra Shill Pintu. "HapPart: partitioning algorithm for multiple haplotyping from haplotype conflict graph." International Journal of Electrical and Computer Engineering (IJECE) 12, no. 3 (2022): 2856–66. https://doi.org/10.11591/ijece.v12i3.pp2856-2866.

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Each chromosome in the human genome has two copies. The haplotype assembly challenge entails reconstructing two haplotypes (chromosomes) using aligned fragments genomic sequence. Plants viz. wheat, paddy and banana have more than two chromosomes. Multiple haplotype reconstruction has been a major research topic. For reconstructing multiple haplotypes for a polyploid organism, several approaches have been designed. The researchers are still fascinated to the computational challenge. This article introduces a partitioning algorithm, HapPart for dividing the fragments into k-groups focusing on re

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Chu, Wai Keung, Peter Edge, Ho Suk Lee, et al. "Ultraaccurate genome sequencing and haplotyping of single human cells." Proceedings of the National Academy of Sciences 114, no. 47 (2017): 12512–17. http://dx.doi.org/10.1073/pnas.1707609114.

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Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microflu

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Newman, Chris, Ming-shan Tsai, Christina D. Buesching, Peter W. H. Holland, and David W. Macdonald. "The genome sequence of the European badger, Meles meles (Linnaeus, 1758)." Wellcome Open Research 7 (September 23, 2022): 239. http://dx.doi.org/10.12688/wellcomeopenres.18230.1.

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We present a haplotype resolved, diploid genome assembly from a male Meles meles (European badger; Chordata; Mammalia; Carnivora; Mustelidae) using the trio binning approach. The genome sequence is 2,739 megabases in span. The majority of the assembly (95.16%) is scaffolded into 23 chromosomal pseudomolecules with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length.

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Si, Hongbo, Haris Vikalo, and Sriram Vishwanath. "Information-Theoretic Analysis of Haplotype Assembly." IEEE Transactions on Information Theory 63, no. 6 (2017): 3468–79. http://dx.doi.org/10.1109/tit.2017.2686884.

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Mousavi, Sayyed R. "Improved haplotype assembly using Xor genotypes." Journal of Theoretical Biology 298 (April 2012): 122–30. http://dx.doi.org/10.1016/j.jtbi.2012.01.003.

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Henglin, Mir, Maryam Ghareghani, William T. Harvey, et al. "Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing." Genome Biology 25, no. 1 (2024). http://dx.doi.org/10.1186/s13059-024-03409-1.

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Abstract Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplotype-collapsed assembly. Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology to produce chromosome-scale de novo haplotypes for diploid genomes. Graphasing readily integrates with any assembly workflow that both outputs an assembly graph and has a haplotype assembly mode. Grapha

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Li, Taotao, Duo Du, Dandan Zhang, et al. "CRISPR-based targeted haplotype-resolved assembly of a megabase region." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-022-35389-w.

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AbstractConstructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region

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Consul, Shorya, Ziqi Ke, and Haris Vikalo. "XHap: Haplotype Assembly Using Long-Distance Read Correlations Learned by Transformers." Bioinformatics Advances, November 23, 2023. http://dx.doi.org/10.1093/bioadv/vbad169.

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Abstract Reconstructing haplotypes of an organism from a set of sequencing reads is a computationally challenging (NP-hard) problem. In reference-guided settings, at the core of haplotype assembly is the task of clustering reads according to their origin, i.e., grouping together reads that sample the same haplotype. Read length limitations and sequencing errors render this problem difficult even for diploids; the complexity of the problem grows with the ploidy of the organism. We present XHap, a novel method for haplotype assembly that aims to learn correlations between pairs of sequencing rea

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