Results 11 to 20 of about 296,746 (277)

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

Gigascience, 2021
Long-read sequencing has enabled unprecedented surveys of structural variation across the entire human genome. To maximize the potential of long-read sequencing in this context, novel mapping methods have emerged that have primarily focused on either ...
Fu Y, Mahmoud M, Muraliraman VV, Sedlazeck FJ, Treangen TJ.   +4 more
europepmc   +4 more sources

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

Nucleic Acids Res, 2020
The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies
Prodanov T, Bansal V.
europepmc   +4 more sources

ESKEMAP: exact sketch-based read mapping

Algorithms for Molecular Biology
Background Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a “similar sequence”. Traditionally, “similar sequence” was defined as having a high alignment score and read mappers were ...
Tizian Schulz, Paul Medvedev
doaj   +2 more sources

Accurate Long Read Mapping using Enhanced Suffix Arrays. [PDF]

Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, 2011
With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs.
Vyverman, Michaël, De Schrijver, Joachim, Van Criekinge, Wim, Dawyndt, Peter, Fack, Veerle   +4 more
core   +4 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

Exact Sketch-Based Read Mapping [PDF]

, 2023
Schulz T, Medvedev P. Exact Sketch-Based Read Mapping. bioRxiv. 2023.Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a "similar sequence".
Medvedev, Paul, Schulz, Tizian ; https://orcid.org/   +1 more
core   +3 more sources

Stranded Mapping from Oriented Long Reads v7 [PDF]

, 2020
This protocol demonstrates how to map strand-oriented long reads to a genome, and visualise them in a genome browser. The general idea is to use minimap2 to create stranded BAM files, which are split for forward/reverse orientation then converted into BigWig format for display in a genome browser.
  +10 more sources

Long-Read Transcriptome of Equine Bronchoalveolar Cells [PDF]

, 2022
We used Pacific Biosciences long-read isoform sequencing to generate full-length transcript sequences in equine bronchoalveolar lavage fluid (BALF) cells. Our dataset consisted of 313,563 HiFi reads comprising 805 Mb of polished sequence information. The
Vidhya Jagannathan, Sage, Sophie Elena, Pamela Nicholson, Nicholson, Pamela, Jagannathan, Vidhya, Sophie Elena Sage, Leeb, Tosso, Tosso Leeb, Gerber, Vinzenz, Vinzenz Gerber   +9 more
core   +1 more source

Complementarity of Long‐Reads and Optical Mapping in Parkinson's Disease for Structural Variants

Annals of Clinical and Translational Neurology
ABSTRACT Objective Long‐read sequencing and optical genome mapping technologies have the ability to detect large and complex structural variants. This has led to the discovery of novel pathogenic variants in neurodegenerative movement disorders.
André Fienemann, Theresa Lüth, Susen Schaake, Carolin Gabbert, Marius Möller, Hauke Busch, Katja Lohmann, Jonas A. Gustafson, Danny E. Miller, Kensuke Daida, Manabu Funayama, Nobutaka Hattori, Samia Ben Sassi, Faycel Hentati, Matthew J. Farrer, Kristian K. Ullrich, Christine Klein, Joanne Trinh   +17 more
openaire   +4 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