Results 31 to 40 of about 141,521 (289)

Genome-wide significance for dense SNP and resequencing data. [PDF]

, 2008
The problem of multiple testing is an important aspect of genome-wide association studies, and will become more important as marker densities increase.
Whittaker, John C, De Iorio, Maria, Hoggart, Clive J, Clark, Taane G, Balding, David J   +4 more
core   +1 more source

ALLPATHS: de novo assembly of whole-genome shotgun microreads [PDF]

, 2008
New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce.
Kleber, M, Nusbaum, C, MacCallum, I, Jaffe, DB, Lander, ES, Shlyakhter, IA, Belmonte, MK, Butler, J   +7 more
core   +1 more source

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Genome Biology, 2020
Background The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias ...
Danang Crysnanto, Hubert Pausch
doaj   +1 more source

A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes

BMC Bioinformatics, 2021
Background With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great ...
Jindan Guo, Erli Pang, Hongtao Song, Kui Lin   +3 more
doaj   +1 more source

G-Graph: An interactive genomic graph viewer [PDF]

, 2019
Abstract Motivation Effective and efficient exploration of numeric data and annotations as a function of genomic position requires specialized software. Results We present G-Graph, an interactive genomic scatter plot viewer.
Andrews, Peter A., Alexander, Joan, Kendall, Jude, Wigler, Michael   +3 more
openaire   +1 more source

FORGe: prioritizing variants for graph genomes [PDF]

Genome Biology, 2018
Abstract There is growing interest in using genetic variants to augment the reference genome into a “graph genome” to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment-score penalty, it also increases both the ambiguity of the reference genome and
Jacob Pritt, Nae-Chyun Chen, Ben Langmead   +2 more
openaire   +3 more sources

Draft genome sequence of the earliest Cronobacter sakazakii sequence type 4 strain, NCIMB 8272 [PDF]

, 2013
The Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is associated with severe cases of neonatal meningitis and persistence in powdered infant formula.
Forsythe, S, Hariri, S, Farbos, A, McNally, A, Moore, K, Paszckiewicz, K, Masood, N, Dickins, B   +7 more
core   +1 more source

Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies [PDF]

, 2008
Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants, which is a plausible scenario for many complex diseases.
Maria De Iorio, John C Whittaker, Balding, DJ, De Iorio Maria, Clive J. Hoggart, Hoggart, Clive J, Balding, David J, David J Balding, Clive J Hoggart, Whittaker, John C, Balding David J., De Iorio, Maria, John C. Whittaker, Whittaker John C., De Iorio, M, Whittaker, JC, Hoggart Clive J., Hoggart, CJ, David J. Balding   +18 more
core   +1 more source

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies [version 2; referees: 2 approved]

F1000Research, 2018
Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved analysis
Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan Dunn, Andrew Olson, Ben Busby, Alexander T. Dilthey   +7 more
doaj   +1 more source

Genome sequence of the Chlamydophila abortus variant strain LLG [PDF]

, 2011
Chlamydophila abortus is a common cause of ruminant abortion. Here we report the genome sequence of strain LLG, which differs genotypically and phenotypically from the wild-type strain S26/3.
Clark, Ewan M., Smith, David George Emslie, Longbottom, D., David G. E. Smith, Spalding, L., Livingstone, M., Vretou, E., Clark, E.M., David Longbottom, Longbottom, David, Lainson, Alex F., Lainson, F.A., Victoria I. Siarkou, Wheelhouse, Nick M., Morag Livingstone, Spalding, Lucy, Wheelhouse, Nick, Lainson, F Alex, Michelle Sait, Wheelhouse, N., Lucy Spalding, Siarkou, Victoria I, Sait, M., Ewan M. Clark, F. Alex Lainson, Siarkou, V.I., Evangelia Vretou, Siarkou, Victoria I., Smith, David, Sait, Michelle, Clark, Ewan M, Nick Wheelhouse, Livingstone, Morag, Smith, David G E, Smith, D.G.E., Vretou, Evangelia   +35 more
core   +1 more source