Results 31 to 40 of about 672,449 (294)

Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing [PDF]

, 2017
Compared with conventional methods, single-molecule real-time (SMRT) DNA sequencing exhibits longer read lengths than conventional methods, less GC bias, and the ability to read DNA base modifications.
Henley, Robert Y., Jadhav, Vivek, Korlach, Jonas, Larkin, Joseph, Wanunu, Meni   +4 more
core   +1 more source

InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. [PDF]

, 2016
Phasing of single nucleotide (SNV), and structural variations into chromosome-wide haplotypes in humans has been challenging, and required either trio sequencing or restricting phasing to population-based haplotypes.
Bafna, Vineet, Bansal, Vikas, Edge, Peter, Patel, Anand, Selvaraj, Siddarth   +4 more
core   +2 more sources

Long-Read Sequencing Annotation of the Transcriptome in DNA-PK Inactivated Cells

Frontiers in Oncology, 2022
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) with a Ku70/Ku80 heterodimer constitutes the intact DNA-PK kinase, which is an upstream component of the DNA repair machinery that signals the DNA damage, orchestrates the DNA repair, and ...
Liwei Song, Liwei Song, Mengjun Yu, Renjing Jin, Meng Gu, Ziyu Wang, Dailun Hou, Shaofa Xu, Jinghui Wang, Jinghui Wang, Teng Ma   +10 more
doaj   +1 more source

Haplotype-phased synthetic long reads from short-read sequencing

PLOS ONE, 2015
AbstractNext-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in ...
Stapleton, James A, Kim, Jeongwoon, Hamilton, John P, Wu, Ming, Irber, Luiz C, Maddamsetti, Rohan, Briney, Bryan, Newton, Linsey, Burton, Dennis R, Brown, C Titus, Chan, Christina, Buell, C Robin, Whitehead, Timothy A   +12 more
openaire   +6 more sources

Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales

Applications in Plant Sciences, 2023
Premise We present approaches used to generate long‐read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output.
Gisel Y. De La Cerda, Jacob B. Landis, Evan Eifler, Adriana I. Hernandez, Fay‐Wei Li, Jing Zhang, Carrie M. Tribble, Nisa Karimi, Patricia Chan, Thomas Givnish, Susan R. Strickler, Chelsea D. Specht   +11 more
doaj   +1 more source

Hybrid assembly with long and short reads improves discovery of gene family expansions [PDF]

, 2017
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation.
Denny, R., Gurtowski, J., Lee, H., Liu, J., Maron, L. G., McCombie, W. R., McCouch, S. R., Miller, J. R., Mudge, J., Ramaraj, T., Schatz, M. C., Silverstein, K. A. T., Singh, N., Song, L., Stupar, R. M., Tiffin, P., Walenz, B. P., Young, N. D., Zhou, P.   +18 more
core   +1 more source

Discovery of large genomic inversions using long range information. [PDF]

, 2017
BackgroundAlthough many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem.
Alkan, Can, Amemiya, Chris T, Antonacci, Francesca, Chiatante, Giorgia, Eichler, Evan E, Eslami Rasekh, Marzieh, Miroballo, Mattia, Tang, Joyce, Ventura, Mario   +8 more
core   +3 more sources

Ultraaccurate genome sequencing and haplotyping of single human cells. [PDF]

, 2017
Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short ...
Bafna, Vineet, Bansal, Vikas, Chu, Wai Keung, Edge, Peter, Huang, Xiaohua, Lee, Ho Suk, Zhang, Kun   +6 more
core   +1 more source

NanoPack: visualizing and processing long read sequencing data [PDF]

Bioinformatics, 2017
AbstractSummary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 Licence.
De Coster, Wouter, D’Hert, Svenn, Schultz, Darrin T., Cruts, Marc, Van Broeckhoven, Christine   +4 more
openaire   +3 more sources

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. [PDF]

, 2020
Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits.
Andrés, Aida M, Dennis, Megan Y, Kaya, Gulhan, Mastoras, Mira, Sahasrabudhe, Ruta, Schmidt, Joshua M, Shew, Colin, Soto, Daniela C   +7 more
core   +3 more sources