Results 31 to 40 of about 111,403 (262)

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

BMC Genomics, 2018
Background De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera ‘Sultanina’ genome assemblies for comparison with the inbred V. vinifera (
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y. Fennell   +5 more
doaj   +1 more source

Haploflow: strain-resolved de novo assembly of viral genomes [PDF]

Genome Biology, 2021
Abstract With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm.
A. Fritz, A. Bremges, Z.-L. Deng, T.-R. Lesker, J. Götting, T. Ganzenmüller, A. Sczyrba, A. Dilthey, F. Klawonn, A.C. McHardy   +9 more
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Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

BMC Biology, 2017
Background The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications.
Peter A. Larsen, R. Alan Harris, Yue Liu, Shwetha C. Murali, C. Ryan Campbell, Adam D. Brown, Beth A. Sullivan, Jennifer Shelton, Susan J. Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C. Durand, Muhammad S. Shamim, Erez Lieberman Aiden, Donna M. Muzny, Richard A. Gibbs, Anne D. Yoder, Jeffrey Rogers, Kim C. Worley   +19 more
doaj   +1 more source

De novo assembly and annotation of the Ganoderma australe genome

Genomics, 2020
The Ganoderma genus represents clear biotechnological potential, due to the large quantity of molecules with biological activity that could be explored. However, available information regarding the biotechnological importance of species within Ganoderma, other than G. lucidum, is quite limited.
Daniel, Agudelo-Valencia, Paula Tatiana, Uribe-Echeverry, John Fredy, Betancur-Pérez   +2 more
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The sequence and de novo assembly of Oxygymnocypris stewartii genome [PDF]

Scientific Data, 2019
AbstractAnimal genomes in the Qinghai-Tibetan Plateau provide valuable resources for scientists to understand the molecular mechanism of environmental adaptation. Tibetan fish species play essential roles in the local ecology; however, the genomic information for native fishes was still insufficient.
Liu, Hai-Ping, Xiao, Shi-Jun, Wu, Nan, Wang, Di, Liu, Yan-Chao, Zhou, Chao-Wei, Liu, Qi-Yong, Yang, Rui-Bin, Jiang, Wen-Kai, Liang, Qi-Qi, Wangjiu, , Zhang, Chi, Gong, Jun-Hua, Yuan, Xiao-Hui, Mou, Zhen-Bo   +14 more
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De novo Genome Assembly of the Raccoon Dog (Nyctereutes procyonoides) [PDF]

Frontiers in Genetics, 2021
The raccoon dog, Nyctereutes procyonoides (NCBI Taxonomy ID: 34880, Figure 1a) belongs to the family Canidae, with foxes (genus Vulpes) being their closest relatives (Lindblad-Toh et al., 2005; Sun et al., 2019). Its original distribution in East Asia ranges from south-eastern Siberia to northern Vietnam and the Japanese islands.
Luis J. Chueca, Luis J. Chueca, Judith Kochmann, Judith Kochmann, Tilman Schell, Carola Greve, Axel Janke, Axel Janke, Axel Janke, Markus Pfenninger, Markus Pfenninger, Markus Pfenninger, Sven Klimpel, Sven Klimpel, Sven Klimpel   +14 more
openaire   +5 more sources

Kermit: linkage map guided long read assembly

Algorithms for Molecular Biology, 2019
Background  With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost.
Riku Walve, Pasi Rastas, Leena Salmela
doaj   +1 more source

An Integrated Pipeline for de Novo Assembly of Microbial Genomes [PDF]

PLoS ONE, 2012
Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence ...
Tritt, Andrew, Eisen, Jonathan A, Facciotti, Marc T, Darling, Aaron E   +3 more
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Methods for De-novo Genome Assembly

, 2020
Despite advances in algorithms and computational platforms, de-novo genome assembly remains a challenging process. Due to the constant innovation in sequencing technologies (Sanger, SOLiD, Illumina, 454, PacBio and Oxford Nanopore), genome assembly has evolved to respond to the changes in input data type.
Arash Bayat, Hasindu Gamaarachchi, Nandan P. Deshpande, Marc R. Wilkins, Sri Parameswaran   +4 more
openaire   +2 more sources

The sequence and de novo assembly of the giant panda genome [PDF]

Nature, 2009
Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats.
Li, Ruiqiang, Fan, Wei, Tian, Geng, Zhu, Hongmei, He, Lin, Cai, Jing, Huang, Quanfei, Cai, Qingle, Li, Bo, Bai, Yinqi, Zhang, Zhihe, Zhang, Yaping, Wang, Wen, Li, Jun, Wei, Fuwen, Li, Heng, Jian, Min, Li, Jianwen, Zhang, Zhaolei, Nielsen, Rasmus, Li, Dawei, Gu, Wanjun, Yang, Zhentao, Xuan, Zhaoling, Ryder, Oliver A., Leung, Frederick Chi-Ching, Zhou, Yan, Cao, Jianjun, Sun, Xiao, Fu, Yonggui, Fang, Xiaodong, Guo, Xiaosen, Wang, Bo, Hou, Rong, Shen, Fujun, Mu, Bo, Ni, Peixiang, Lin, Runmao, Qian, Wubin, Wang, Guodong, Yu, Chang, Nie, Wenhui, Wang, Jinhuan, Wu, Zhigang, Liang, Huiqing, Min, Jiumeng, Wu, Qi, Cheng, Shifeng, Ruan, Jue, Wang, Mingwei, Shi, Zhongbin, Wen, Ming, Liu, Binghang, Ren, Xiaoli, Zheng, Huisong, Dong, Dong, Cook, Kathleen, Shan, Gao, Zhang, Hao, Kosiol, Carolin, Xie, Xueying, Lu, Zuhong, Zheng, Hancheng, Li, Yingrui, Steiner, Cynthia C., Lam, Tommy Tsan-Yuk, Lin, Siyuan, Zhang, Qinghui, Li, Guoqing, Tian, Jing, Gong, Timing, Liu, Hongde, Zhang, Dejin, Fang, Lin, Ye, Chen, Zhang, Juanbin, Hu, Wenbo, Xu, Anlong, Ren, Yuanyuan, Zhang, Guojie, Bruford, Michael W., Li, Qibin, Ma, Lijia, Guo, Yiran, An, Na, Hu, Yujie, Zheng, Yang, Shi, Yongyong, Li, Zhiqiang, Liu, Qing, Chen, Yanling, Zhao, Jing, Qu, Ning, Zhao, Shancen, Tian, Feng, Wang, Xiaoling, Wang, Haiyin, Xu, Lizhi, Liu, Xiao, Vinar, Tomas, Wang, Yajun, Lam, Tak-Wah, Yiu, Siu-Ming, Liu, Shiping, Zhang, Hemin, Li, Desheng, Huang, Yan, Wang, Xia, Yang, Guohua, Jiang, Zhi, Wang, Junyi, Qin, Nan, Li, Li, Li, Jingxiang, Bolund, Lars, Kristiansen, Karsten, Wong, Gane Ka-Shu, Olson, Maynard, Zhang, Xiuqing, Li, Songgang, Yang, Huanming, Wang, Jian, Wang, Jun   +122 more
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