Relevant bibliographies by topics / Haplotype assembly

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  2. Dissertations / Theses
  3. Book chapters
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Academic literature on the topic 'Haplotype assembly'

Author: Grafiati
Published: 9 March 2023
Last updated: 31 July 2025

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Journal articles on the topic "Haplotype assembly"

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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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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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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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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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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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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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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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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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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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Dissertations / Theses on the topic "Haplotype assembly"

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Faure, Roland. "Haplotype assembly from long reads." Electronic Thesis or Diss., Université de Rennes (2023-....), 2024. http://www.theses.fr/2024URENS052.

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Cette thèse propose des solutions pour améliorer l'assemblage des génomes à partir de lectures de séquençage de troisième génération (lectures longues). Plus précisément, elle se concentre sur l'amélioration de l'assemblage des (méta)génomes contenant plusieurs haplotypes, comme des génomes polyploïdes ou des souches bactériennes proches. Les assembleurs actuels ont du mal à séparer les haplotypes très similaires, et fusionnent généralement des (parties d')haplotypes, ce qui entraîne la perte de polymorphismes et d'hétérozygotie dans l'assemblage final. Ce travail présente une série de méthode
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Moeinzadeh, Mohammadhossein [Verfasser]. "De novo and haplotype assembly of polyploid genomes / Mohammadhossein Moeinzadeh." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1189660237/34.

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ZACCARIA, SIMONE. "Inferring Genomic Variants and their Evolution: Combinatorial Optimization for Haplotype Assembly and Quantification of Intra-Tumor Heterogeneity." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2017. http://hdl.handle.net/10281/151631.

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Il genoma di ogni individuo nella popolazione umana è caratterizzato univocamente da un insieme di varianti genomiche che distinguono il suo DNA da ogni altro. Perciò, studiare la relazione tra queste varianti e le differenze osservabili negli individui è fondamentale per molte applicazioni mediche. Per identificare queste varianti, le tecnologie di sequenziamento producono un’enorme quantità di frammenti di DNA. Tuttavia, questi frammenti danno solo una visione approssimativa del DNA di un individuo, perché sono molto più corti, contengono diversi errori e sono ottenuti considerando milioni d
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Price, Jared Calvin. "The Bioluminescence Heterozygous Genome Assembler." BYU ScholarsArchive, 2014. https://scholarsarchive.byu.edu/etd/4346.

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High-throughput DNA sequencing technologies are currently revolutionizing the fields of biology and medicine by elucidating the structure and function of the components of life. Modern DNA sequencing machines typically produce relatively short reads of DNA which are then assembled by software in an attempt to produce a representation of the entire genome. Due to the complex structure of all but the smallest genomes, especially the abundant presence of exact or almost exact repeats, all genome assemblers introduce errors into the final sequence and output a relatively large set of contigs inste
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TANGHERLONI, ANDREA. "High-Performance Computing to tackle complex problems in life sciences." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2019. http://hdl.handle.net/10281/241217.

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Nuovi ed efficienti metodi computazionali sono attualmente necessari per elaborare la ingente mole di dati generata dalle più recenti tecnologie sviluppate in svariati settori delle scienze della vita, tra cui la biologia computazionale e l’imaging medicale. In altre discipline, come la biologia dei sistemi in cui si modellano matematicamente le reti biochimiche, è necessario affrontare problemi relativi alla mancanza di dati quantitativi, e allo stesso tempo simulare efficacemente le dinamiche emergenti di queste reti. In questi contesti applicativi, le infrastrutture di calcolo ad elevate p
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Yang, Ei Wen, and 楊翊文. "The Extension of Algorithms for Single Nucleotide Polymorphism Haplotype Assembly Problems." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/87857613803901359159.

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碩士<br>國立清華大學<br>資訊工程學系<br>93<br>Single nucleotide polymorphisms (SNPs) is one of the most considered topics. This phenomenon of genetic polymorphism is the most frequent human genetic variation and corresponding to numerous applications such as medical diagnosis, drug design and phylogenis. It is also helpful for tracking disease genes. The complete sequence of SNP varieties from a single copy of chromosomes is called a haplotype. To determine haplotypes for a single individual, one alternative method proposed in [1, 2] is based on the DNA fragments and the methodology of Shotgun Sequencing As
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Chuang, Shengyu, and 莊盛宇. "Simultaneous Haplotype Assembly and Structural Variations Detection Using Next Generation Sequencing." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/53850063627106944834.

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碩士<br>國立中正大學<br>資訊工程研究所<br>100<br>The genomes of most species in the biosphere is a diploid genome composed of two haplotypes. However, existing short-read assemblers for next-generation sequencing (NGS) platforms only reconstruct one consensus sequence which is a mosaic of the two haplotypes. In addition, the differences between the two haplotypes range from Single Nucleotide Polymorphisms (SNPs) to large-scale structure variations (SVs). Therefore, de novo haplotype assembly of a diploid genome is a still challenging task using NGS platforms. In this thesis, we design and implement a new fra
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Book chapters on the topic "Haplotype assembly"

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Aldinucci, Marco, Andrea Bracciali, Tobias Marschall, Murray Patterson, Nadia Pisanti, and Massimo Torquati. "High-Performance Haplotype Assembly." In Computational Intelligence Methods for Bioinformatics and Biostatistics. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-24462-4_21.

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Patterson, Murray, Tobias Marschall, Nadia Pisanti, et al. "WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads." In Lecture Notes in Computer Science. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-05269-4_19.

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Sun, Hequan, José A. Campoy, and Korbinian Schneeberger. "Gamete Binning to Achieve Haplotype-Resolved Genome Assembly." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2819-5_13.

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Battistella, Enzo, Anant Maheshwari, Barış Ekim, Bonnie Berger, and Victoria Popic. "ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly." In Lecture Notes in Computer Science. Springer Nature Switzerland, 2025. https://doi.org/10.1007/978-3-031-90252-9_37.

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Wu, Shan, Mercy Kitavi, John P. Hamilton, C. Robin Buell, and Zhangjun Fei. "US Efforts in Sweetpotato Genome Sequencing: Advances in the Development of Reference Genomes to Facilitate Research and Breeding of a Key Food Security Crop." In Compendium of Plant Genomes. Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-65003-1_2.

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AbstractGenomic information provides a fundamental tool for modern crop breeding. Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important crop. However, the genome of sweetpotato is understudied due to its highly heterozygous hexaploid nature, preventing straightforward access to its genomic landscape. Here, we summarize the previous and on-going efforts in the US in the development of reference genomes for sweetpotato. Genomeassemblies of diploid wild relatives, I. trifida and I. triloba, were first generated to serve as robust references for the hexaploid cultivated sweetpotato. Taki
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HALLDÓRSSON, BJARNI V., DEREK AGUIAR, and SORIN ISTRAIL. "HAPLOTYPE PHASING BY MULTI-ASSEMBLY OF SHARED HAPLOTYPES: PHASE-DEPENDENT INTERACTIONS BETWEEN RARE VARIANTS." In Biocomputing 2011. WORLD SCIENTIFIC, 2010. http://dx.doi.org/10.1142/9789814335058_0010.

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Conference papers on the topic "Haplotype assembly"

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Dubovskova, S. D., and A. A. Zamyatin. "VALIDATION OF A. COLUZZII AND A. GAMBIAE HYBRIDS HAPLOTYPE PHASING BY TRIO BINNING." In XI МЕЖДУНАРОДНАЯ КОНФЕРЕНЦИЯ МОЛОДЫХ УЧЕНЫХ: БИОИНФОРМАТИКОВ, БИОТЕХНОЛОГОВ, БИОФИЗИКОВ, ВИРУСОЛОГОВ, МОЛЕКУЛЯРНЫХ БИОЛОГОВ И СПЕЦИАЛИСТОВ ФУНДАМЕНТАЛЬНОЙ МЕДИЦИНЫ. IPC NSU, 2024. https://doi.org/10.25205/978-5-4437-1691-6-2.

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The majority of nowadays genome assemblies are mixed haplotypes. An assembly of such haplotypes introduces DNA variants not present in any of true haplotypes, which negatively affects downstream genome analysis. Therefore, we assembled phased haplotypes of major malaria vectors in Sub-Saharan Africa using trio binning method. To validate haplotype phasing, we performed p-distance and k-mer quotient analyses. The results indicate correct haplotypes phasing.
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Si, Hongbo, Haris Vikalo, and Sriram Vishwanath. "Haplotype assembly: An information theoretic view." In 2014 IEEE Information Theory Workshop (ITW). IEEE, 2014. http://dx.doi.org/10.1109/itw.2014.6970817.

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Das, Shreepriya, and Haris Vikalo. "Optimal haplotype assembly with statistical pruning." In 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP). IEEE, 2014. http://dx.doi.org/10.1109/globalsip.2014.7032339.

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AGUIAR, DEREK, WENDY S. W. WONG, and SORIN ISTRAIL. "TUMOR HAPLOTYPE ASSEMBLY ALGORITHMS FOR CANCER GENOMICS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2013. http://dx.doi.org/10.1142/9789814583220_0002.

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Zhao, Yuying, and Jinshan Li. "Label Propagation Algorithm for Haplotype Assembly Problem." In 2015 4th International Conference on Mechatronics, Materials, Chemistry and Computer Engineering. Atlantis Press, 2015. http://dx.doi.org/10.2991/icmmcce-15.2015.385.

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Puljiz, Zrinka, and Haris Vikalo. "A message passing algorithm for haplotype assembly." In 2013 Asilomar Conference on Signals, Systems and Computers. IEEE, 2013. http://dx.doi.org/10.1109/acssc.2013.6810596.

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"Haplotype-Resolved genome assembly of the Microvine." In Open-GPB. International Viticulture and Enology Society, 2024. http://dx.doi.org/10.58233/gsqdlbuj.

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Moeinzadeh, M.-Hossein, Ehsan Asgariarn, Morteza Mohammad Noori, Mehdi Sadeghi, and Sara Sharifian-R. "F.C.A: Designing a fuzzy clustering algorithm for haplotype assembly." In 2009 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE). IEEE, 2009. http://dx.doi.org/10.1109/fuzzy.2009.5277349.

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Kamath, Govinda M., Eren Sasoglu, and David Tse. "Optimal haplotype assembly from high-throughput mate-pair reads." In 2015 IEEE International Symposium on Information Theory (ISIT). IEEE, 2015. http://dx.doi.org/10.1109/isit.2015.7282588.

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Wu, Jingli, Jianxin Wang, and Jian'er Chen. "A Genetic Algorithm for Single Individual SNP Haplotype Assembly." In 2008 9th International Conference for Young Computer Scientists (ICYCS). IEEE, 2008. http://dx.doi.org/10.1109/icycs.2008.95.

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Reports on the topic "Haplotype assembly"

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Weng, Ziqing, Dorian J. Garrick, Mahdi Saatchi, Robert Schnabel, and Jeremy Taylor. Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle. Iowa State University, 2013. http://dx.doi.org/10.31274/ans_air-180814-632.

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