Results 1 to 10 of about 1,004,545 (280)

High-resolution mapping of reciprocal translocation breakpoints using long-read sequencing

MethodsX, 2019
Long-read nanopore sequencing enables direct high-resolution breakpoint mapping on balanced carriers of reciprocal translocation. The mean sequencing depth on the translocated chromosomes to achieve accurate mapping of breakpoints ranged from 2.5-fold to
Judy F.C. Chow, Heidi H.Y. Cheng, Estella Y.L. Lau, William S.B. Yeung, Ernest H.Y. Ng   +4 more
doaj   +5 more sources

Long-read mapping to repetitive reference sequences using Winnowmap2. [PDF]

Nat Methods, 2022
Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias.
Jain C, Rhie A, Hansen NF, Koren S, Phillippy AM.   +4 more
europepmc   +4 more sources

Comparison of whole genome sequencing approaches for Capripox viruses [PDF]

BMC Genomics
Background Direct whole genome sequencing of Capripox virus genomes from diagnostic samples is not always straightforward. Low viral content in a sample, biased sequencing and subsequent assembly and mapping methods may all influence the outcome. Methods
Floris C. Breman, Stefan Hoffman, Andy Haegeman, Wannes Philips, Sigrid de Keersmaecker, Patrick Mileto, Matthew J. Neave, Timothy R. Bowden, Tirumala B.K. Settypalli, Charles E. Lamien, Carrie Batten, Caroline Wright, Nick De Regge   +12 more
doaj   +2 more sources

Density-reducing Jaccard estimators for sketch-based long read applications [PDF]

BMC Bioinformatics
Sequence sketching—a class of techniques aimed at generating compact representations of longer sequences—has become widely used in numerous long read applications, including assembly and mapping.
Tazin Rahman, Ananth Kalyanaraman
doaj   +2 more sources

Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants [PDF]

BMC Genomics
Accurate characterization of genetic variation is fundamental to genomics. While long-read sequencing technologies promise to resolve complex genomic regions and improve variant detection, their application in complex genomes has not been well validated.
Yoshinori Fukasawa
doaj   +2 more sources

Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. [PDF]

Gigascience, 2021
Fu Y, Mahmoud M, Muraliraman VV, Sedlazeck FJ, Treangen TJ.   +4 more
europepmc   +2 more sources

Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications. [PDF]

Nucleic Acids Res, 2020
Prodanov T, Bansal V.
europepmc   +2 more sources

Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping

Scientific Reports
Structural variants (SVs) are important contributors to human disease. Their characterization remains however difficult due to their size and association with repetitive regions.
Griet De Clercq, Lies Vantomme, Barbara Dewaele, Bert Callewaert, Olivier Vanakker, Sandra Janssens, Bart Loeys, Mojca Strazisar, Wouter De Coster, Joris Robert Vermeesch, Annelies Dheedene, Björn Menten   +11 more
doaj   +2 more sources

Long-read technologies identify a hidden inverted duplication in a family with choroideremia

HGG Advances, 2021
Summary: The lack of molecular diagnoses in rare genetic diseases can be explained by limitations of current standard genomic technologies. Upcoming long-read techniques have complementary strengths to overcome these limitations, with a particular ...
Zeinab Fadaie, Kornelia Neveling, Tuomo Mantere, Ronny Derks, Lonneke Haer-Wigman, Amber den Ouden, Michael Kwint, Luke O’Gorman, Dyon Valkenburg, Carel B. Hoyng, Christian Gilissen, Lisenka E.L.M. Vissers, Marcel Nelen, Frans P.M. Cremers, Alexander Hoischen, Susanne Roosing   +15 more
doaj   +1 more source

Re-examination of two diatom reference genomes using long-read sequencing

BMC Genomics, 2021
Background The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group.
Gina V. Filloramo, Bruce A. Curtis, Emma Blanche, John M. Archibald   +3 more
doaj   +1 more source