Results 31 to 40 of about 566,210 (290)

Short Read (Next-Generation) Sequencing [PDF]

Circulation: Cardiovascular Genetics, 2013
Rapid advances in DNA sequencing technologies have made it increasingly cost-effective to obtain accurate and timely large-scale genomic sequence data on individuals (short read massively parallel or next generation [next-gen]). A next-gen molecular diagnostic approach that has seen rapid deployment in the clinic over the last year is exome sequencing.
Jaya, Punetha, Eric P, Hoffman
openaire   +2 more sources

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

BMC Microbiology, 2021
Background Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the ...
Yoshiyuki Matsuo, Shinnosuke Komiya, Yoshiaki Yasumizu, Yuki Yasuoka, Katsura Mizushima, Tomohisa Takagi, Kirill Kryukov, Aisaku Fukuda, Yoshiharu Morimoto, Yuji Naito, Hidetaka Okada, Hidemasa Bono, So Nakagawa, Kiichi Hirota   +13 more
doaj   +1 more source

Detection of microRNAs in color space [PDF]

, 2011
MotivationDeep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of ...
Altschul, Antonio Marco, Applied, Applied, Bartel, Berezikov, Cai, Chen, Cloonan, David, Flicek, Friedlander, Goff, Hofacker, Homer, Kozomara, Langmead, Li, Li, Li, Lowe, Marco, Mardis, Morin, Moxon, Robin, Ruby, Rumble, Sam Griffiths-Jones, Sasson   +29 more
core   +2 more sources

Merging short and stranded long reads improves transcript assembly.

PLoS Computational Biology, 2023
Long-read RNA sequencing has arisen as a counterpart to short-read sequencing, with the potential to capture full-length isoforms, albeit at the cost of lower depth.
Amoldeep S Kainth, Gabriela A Haddad, Johnathon M Hall, Alexander J Ruthenburg   +3 more
doaj   +1 more source

Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

Molecular Genetics & Genomic Medicine, 2020
Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by ...
Kévin Uguen, Claire Jubin, Yannis Duffourd, Claire Bardel, Valérie Malan, Jean‐Michel Dupont, Laila El Khattabi, Nicolas Chatron, Antonio Vitobello, Pierre‐Antoine Rollat‐Farnier, Céline Baulard, Marc Lelorch, Aurélie Leduc, Emilie Tisserant, Frédéric Tran Mau‐Them, Vincent Danjean, Marc Delepine, Marianne Till, Vincent Meyer, Stanislas Lyonnet, Anne‐laure Mosca‐Boidron, Julien Thevenon, Laurence Faivre, Christel Thauvin‐Robinet, Caroline Schluth‐Bolard, Anne Boland, Robert Olaso, Patrick Callier, Serge Romana, Jean‐François Deleuze, Damien Sanlaville   +30 more
doaj   +1 more source

Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

BMC Genomics, 2021
Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis.
Kerstin Neubert, Eric Zuchantke, Robert Maximilian Leidenfrost, Roebbe Wuenschiers, Josephine Grützke, Burkhard Malorny, Holger Brendebach, Sascha Al Dahouk, Timo Homeier, Helmut Hotzel, Knut Reinert, Herbert Tomaso, Anne Busch   +12 more
doaj   +1 more source

GGTyper: genotyping complex structural variants using short-read sequencing data. [PDF]

Bioinformatics
Abstract Motivation Complex structural variants (SVs) are genomic rearrangements that involve multiple segments of DNA. They contribute to human diversity and have been shown to cause Mendelian disease. Nevertheless, our abilities to analyse complex SVs are very limited. As opposed to deletions
Mirus T, Lohmayer R, Döhring C, Halldórsson BV, Kehr B.   +4 more
europepmc   +3 more sources

Phylogenetic placement of short reads without sequence alignment [PDF]

, 2020
AbstractPhylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them need a multiple alignment of the reference sequences as input.
Matthias Blanke, Burkhard Morgenstern
openaire   +1 more source

Genomic sequence characteristics and the empiric accuracy of short-read sequencing [PDF]

, 2021
AbstractBackgroundShort-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias, reduce the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately ...
Maximillian Marin, Roger Vargas, Michael Harris, Brendan Jeffrey, L. Elaine Epperson, David Durbin, Michael Strong, Max Salfinger, Zamin Iqbal, Irada Akhundova, Sergo Vashakidze, Valeriu Crudu, Alex Rosenthal, Maha Reda Farhat   +13 more
openaire   +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