Results 11 to 20 of about 60,554,138 (296)

Exploiting sparseness in de novo genome assembly [PDF]

BMC Bioinformatics, 2012
Background: The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.
Cannon, Charles H, Ma, Zhanshan Sam, Ye, Chengxi, Yu, Douglas W., Zhanshan Ma, Yu, Douglas W, Cannon, Charles H., Pop, Mihai, Douglas W Yu, Mihai Pop, Charles H Cannon, Chengxi Ye, Sam Ma, Zhanshan   +12 more
core   +7 more sources

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
openaire   +2 more sources

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

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.) [PDF]

, 2022
A contiguous assembly of the inbred ‘EL10’ sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540
Mutasa-Göttgens, E. S., Pulman, J., Naegele, R., Galewski, P., Wang, J., Johnson, S., Liu, T., Lee, J., Funk, A., Sullivan, S., Darracq, A., Davenport, K., Ou, S., Childs, K., Willems. G., Barnes, S., Daligault, H., Shu, S., Taguchi, K., Liachko, I., Stevanato, P., Townsend, B. J., Phillippy, A., Dorn, K. M., Hastie, A., Koren, S., Yocum, A., Mitchell McGrath, J.   +27 more
core   +1 more source

Attempts to detect retrotransposition and de novo deletion of Alus and other dispersed repeats at specific loci in the human genome [PDF]

, 2001
Dispersed repeat elements contribute to genome instability by de novo insertion and unequal recombination between repeats. To study the dynamics of these processes, we have developed single DNA molecule approaches to detect de novo insertions at a single
Monckton, D.G., Jeffreys, A.J., Hollies, C.R.   +2 more
core   +9 more sources

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

The sequence and de novo assembly of the wild yak genome [PDF]

Scientific Data, 2020
AbstractVulnerable populations of wild yak (Bos mutus), the wild ancestral species of domestic yak, survive in extremely cold, harsh and oxygen-poor regions of the Qinghai-Tibetan Plateau (QTP) and adjacent high-altitude regions. In this study, we sequenced and assembled its genomede novo.
Liu, Yanbin, Luo, Jiayu, Dou, Jiajia, Yan, Biyao, Ren, Qingmiao, Tang, Bolin, Wang, Kun, Qiu, Qiang   +7 more
openaire   +3 more sources

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
openaire   +2 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