Results 31 to 40 of about 60,554,138 (296)

Genome-scale de novo assembly using ALGA [PDF]

Bioinformatics, 2021
Abstract Motivation There are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage.
Sylwester Swat, Artur Laskowski, Jan Badura, Wojciech Frohmberg, Pawel Wojciechowski, Aleksandra Swiercz, Marta Kasprzak, Jacek Blazewicz   +7 more
openaire   +2 more sources

Scalable De Novo Genome Assembly Using Pregel [PDF]

2018 IEEE 34th International Conference on Data Engineering (ICDE), 2018
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of new genomes.
Da Yan 0001, Hongzhi Chen, James Cheng, Zhenkun Cai, Bin Shao   +4 more
openaire   +2 more sources

De novo genome assembly depicts the immune genomic characteristics of cattle. [PDF]

Nat Commun, 2023
AbstractImmunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb).
Li TT, Xia T, Wu JQ, Hong H, Sun ZL, Wang M, Ding FR, Wang J, Jiang S, Li J, Pan J, Yang G, Feng JN, Dai YP, Zhang XM, Zhou T, Li T.   +16 more
europepmc   +4 more sources

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey [PDF]

, 2009
Background The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome,
Kerstens Hindrik HD, Veenendaal, A., Johan T den Dunnen, Martien AM Groenen, Bert W Dibbits, Thomas FC Chin-A-Woeng, Dunnen, J.T., den, Groenen, M.A.M., Dibbits, B.W., Kerstens, H.H.D., Chin-A-Woeng, T.F.C., Dibbits Bert W, Hindrik HD Kerstens, Richard PMA Crooijmans, Veenendaal Albertine, den Dunnen Johan T, Chin-A-Woeng Thomas FC, Crooijmans, R.P.M.A., Albertine Veenendaal, Groenen Martien AM, Crooijmans Richard PMA, den Dunnen, J.T.   +21 more
core   +1 more source

Extreme-Scale De Novo Genome Assembly [PDF]

, 2017
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code ...
Evangelos Georganas, Steven A. Hofmeyr, Rob Egan, Aydin Buluç, Leonid Oliker, Daniel Rokhsar, Katherine A. Yelick   +6 more
openaire   +2 more sources

Targeted Assembly of Short Sequence Reads [PDF]

, 2011
As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole ...
Rene L. Warren, René L Warren, Robert A Holt, Warren René L., Rene Warren, Holt Robert A., Robert Holt, Robert A. Holt   +7 more
core   +2 more sources

The sequence and de novo assembly of hog deer genome [PDF]

Scientific Data, 2019
AbstractHog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced andde novoassembled its genome sequence in the present study.
Wang, Wei, Yan, Hui-Juan, Chen, Shi-Yi, Li, Zhen-Zhen, Yi, Jun, Niu, Li-Li, Deng, Jia-Po, Chen, Wei-Gang, Pu, Yang, Jia, Xianbo, Qu, Yu, Chen, Ang, Zhong, Yan, Yu, Xin-Ming, Pang, Shuai, Huang, Wan-Long, Han, Yue, Liu, Guang-Jian, Yu, Jian-Qiu   +18 more
openaire   +2 more sources

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

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
openaire   +2 more sources

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