Results 11 to 20 of about 111,403 (262)

De novo genome assemblies of butterflies [PDF]

GigaScience, 2021
Abstract Background The availability of thousands of genomes has enabled new advancements in biology. However, many genomes have not been investigated for their quality. Here we examine quality trends in a taxonomically diverse and well-known group, butterflies (Papilionoidea), and provide draft, de ...
Emily A Ellis, Caroline G Storer, Akito Y Kawahara   +2 more
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Assembler for de novo assembly of large genomes [PDF]

Proceedings of the National Academy of Sciences, 2013
Significance Assembling a large genome faces three challenges: assembly quality, computer memory requirement, and execution time. Our developed assembler, JR-Assembler, uses ( a ) a strategy that selects good seeds for contig construction, ( b
Te-Chin, Chu, Chen-Hua, Lu, Tsunglin, Liu, Greg C, Lee, Wen-Hsiung, Li, Arthur Chun-Chieh, Shih   +5 more
openaire   +2 more sources

Exploiting sparseness in de novo genome assembly [PDF]

BMC Bioinformatics, 2012
The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k- mers as nodes and the links between these nodes allows the de novo ...
Chengxi Ye, Zhanshan (Sam) Ma, Charles H. Cannon, Mihai Pop, Douglas W. Yu   +4 more
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De novo assembly and annotation of the mangrove cricket genome [PDF]

BMC Research Notes, 2021
Abstract Objectives The mangrove cricket, Apteronemobius asahinai, shows endogenous activity rhythms that synchronize with the tidal cycle (i.e., a free-running rhythm with a period of ~ 12.4 h [the circatidal rhythm]). Little is known about the molecular mechanisms underlying the circatidal rhythm.
Aya Satoh, Miwako Takasu, Kentaro Yano, Yohey Terai   +3 more
openaire   +3 more sources

Yet another de novo genome assembler [PDF]

2019 11th International Symposium on Image and Signal Processing and Analysis (ISPA), 2019
Abstract Advances in sequencing technologies have pushed the limits of genome assemblies beyond imagination. The sheer amount of long read data that is being generated enables the assembly for even the largest and most complex organism for which efficient algorithms are needed. We present a new tool, called Ra, for de
Robert Vaser, Mile Sikic
openaire   +2 more sources

De Novo Genome Assembly and Annotation of the Arunachali Yak. [PDF]

Sci Data
The Arunachali yak (Bos grunniens), a high-altitude ruminant endemic to India, is genetically and economically significant for pastoral communities. However, challenges such as population decline, inbreeding, and genetic dilution through crossbreeding threaten its conservation.
Pukhrambam M, Tribhuvan KU, Paul V, Pandey A, Dutta A, Bhadana VP, Dabas S, Ramakrushna GI, Raghavendra KP, Verma P, Prasad YG, Mohanty AK, Rakshit S, Sarkar M.   +13 more
europepmc   +4 more sources

Hardware acceleration of de novo genome assembly [PDF]

International Journal of Embedded Systems, 2017
The cost of genome assembly has gone down drastically with the advent of next generation sequencing technologies. These new sequencing technologies produce large amounts of DNA fragments. Software programs are used to construct the genome from these DNA fragments. The assembly programs take significant amount of time to execute. To reduce the execution
Varma, Sharat Chandra, Kolin, Paul, Balakrishnan, M., Lavenier, Dominique   +3 more
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Metassembler: merging and optimizing de novo genome assemblies [PDF]

Genome Biology, 2015
Abstract Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior ...
Hernandez Wences, Alejandro, Schatz, Michael   +1 more
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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

Comparison of De Novo Assembly Strategies for Bacterial Genomes [PDF]

International Journal of Molecular Sciences, 2021
(1) Background: Short-read sequencing allows for the rapid and accurate analysis of the whole bacterial genome but does not usually enable complete genome assembly. Long-read sequencing greatly assists with the resolution of complex bacterial genomes, particularly when combined with short-read Illumina data.
Pengfei Zhang, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, Zexiao Yang   +5 more
openaire   +2 more sources