Results 1 to 10 of about 452,095 (265)

Bos taurus genome assembly [PDF]

BMC Genomics, 2009
Background We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the ...
Sodergren Erica, Zhang Lan, Ren Yanru, Sodeland Marte, Kent Matthew, Lien Sigbjørn, Durbin K James, Shen Yufeng, Jiang Huaiyang, Song Xing-Zhi, Qin Xiang, Liu Yue, Havlak Paul, Worley Kim C, Weinstock George M, Gibbs Richard A   +15 more
doaj   +4 more sources

Maximum Likelihood Genome Assembly [PDF]

Journal of Computational Biology, 2009
Whole genome shotgun assembly is the process of taking many short sequenced segments (reads) and reconstructing the genome from which they originated. We demonstrate how the technique of bidirected network flow can be used to explicitly model the double-stranded nature of DNA for genome assembly.
Paul Medvedev
exaly   +3 more sources

Genome assembly composition of the String “ACGT” array: a review of data structure accuracy and performance challenges [PDF]

PeerJ Computer Science, 2023
Background The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the ...
Sherif Magdy Mohamed Abdelaziz Barakat, Roselina Sallehuddin, Siti Sophiayati Yuhaniz, Raja Farhana R. Khairuddin, Yasir Mahmood   +4 more
doaj   +2 more sources

Effects of GC bias in next-generation-sequencing data on de novo genome assembly. [PDF]

PLoS ONE, 2013
Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome
Yen-Chun Chen, Tsunglin Liu, Chun-Hui Yu, Tzen-Yuh Chiang, Chi-Chuan Hwang   +4 more
doaj   +1 more source

The MaSuRCA genome assembler [PDF]

Bioinformatics, 2013
Abstract Motivation: Second-generation sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. In particular, multiple algorithms based on de Bruijn graphs have been shown to be effective for the assembly problem.
Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke   +5 more
openaire   +2 more sources

Whole-genome shotgun assembly and comparison of human genome assemblies [PDF]

Proceedings of the National Academy of Sciences, 2004
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries.
Istrail, S., Sutton, G., Florea, L., Halpern, A., Mobarry, C., Lippert, R., Walenz, B., Shatkay, H., Dew, I., Miller, J., Flanigan, M., Edwards, N., Bolanos, R., Fasulo, D., Halldorsson, B., Hannenhalli, S., Turner, R., Yooseph, S., Lu, F., Nusskern, D., Shue, B., Zheng, X., Zhong, F., Delcher, A., Huson, D., Kravitz, S., Mouchard, L., Reinert, K., Remington, K., Clark, A., Waterman, M., Eichler, E., Adams, M., Hunkapiller, M., Myers, E., Venter, J.   +35 more
openaire   +5 more sources

Comparative genome assembly [PDF]

Briefings in Bioinformatics, 2004
One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project.
Mihai Pop, Adam M. Phillippy, Arthur L. Delcher, Steven Salzberg   +3 more
openaire   +3 more sources

The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769 [version 1; peer review: 2 approved]

Wellcome Open Research, 2021
We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules,
Kerstin Howe, Melinda Dwinell, Mary Shimoyama, Craig Corton, Emma Betteridge, Alexander Dove, Michael A. Quail, Michelle Smith, Laura Saba, Robert W. Williams, Hao Chen, Anne E. Kwitek, Shane A. McCarthy, Marcela Uliano-Silva, William Chow, Alan Tracey, James Torrance, Ying Sims, Richard Challis, Jonathan Threlfall, Mark Blaxter   +20 more
doaj   +1 more source

Assembly: a resource for assembled genomes at NCBI [PDF]

Nucleic Acids Research, 2015
The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex ...
Paul A. Kitts, Deanna M. Church, Françoise Thibaud-Nissen, Jinna Choi, Vichet Hem, Victor Sapojnikov, Robert G. Smith 0002, Tatiana A. Tatusova, Charlie Xiang, Andrey Zherikov, Michael DiCuccio, Terence D. Murphy, Kim D. Pruitt, Avi Kimchi   +13 more
openaire   +2 more sources

BlobTools: Interrogation of genome assemblies [PDF]

F1000Research, 2017
The goal of many genome sequencing projects is to provide a complete representation of a target genome (or genomes) as underpinning data for further analyses. However, it can be problematic to identify which sequences in an assembly truly derive from the target genome(s) and which are derived from associated microbiome or contaminant organisms. 
Dominik R. Laetsch, Mark L. Blaxter
openaire   +1 more source