Results 1 to 10 of about 296,746 (277)

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

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   +6 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

Parameterized syncmer schemes improve long-read mapping. [PDF]

PLoS Comput Biol, 2022
Abstract Motivation Sequencing long reads presents novel challenges to mapping. One such challenge is low sequence similarity between the reads and the reference, due to high sequencing error and mutation rates. This occurs, e.g., in a cancer tumor, or due to differences between strains of viruses or
Dutta A, Pellow D, Shamir R.
europepmc   +4 more sources

Weighted minimizer sampling improves long read mapping. [PDF]

Bioinformatics, 2020
Abstract Motivation In this era of exponential data growth, minimizer sampling has become a standard algorithmic technique for rapid genome sequence comparison. This technique yields a sub-linear representation of sequences, enabling their comparison in reduced space and time. A key property of
Jain C, Rhie A, Zhang H, Chu C, Walenz BP, Koren S, Phillippy AM.   +6 more
europepmc   +5 more sources

A survey of mapping algorithms in the long-reads era

Genome Biology, 2023
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to a seed-and ...
Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux, Camille Marchet   +3 more
doaj   +4 more sources

CRISPR-Cas9 enrichment and long read sequencing for fine mapping in plants [PDF]

Plant Methods, 2020
Background Genomic methods for identifying causative variants for trait loci applicable to a wide range of germplasm are required for plant biologists and breeders to understand the genetic control of trait variation. Results We implemented Cas9-targeted
Elena López-Girona, Marcus W. Davy, Nick W. Albert, Elena Hilario, Maia E. M. Smart, Chris Kirk, Susan J. Thomson, David Chagné   +7 more
doaj   +3 more sources

RASSA: Resistive Prealignment Accelerator for Approximate DNA Long Read Mapping [PDF]

IEEE Micro, 2019
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive approximate similarity search accelerator, RASSA, exploits charge distribution and parallel in-memory processing to ...
Roman Kaplan, Leonid Yavits, Ran Ginosar   +2 more
exaly   +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

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases [PDF]

Lecture Notes in Computer Science, 2017
Abstract Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for ...
Alexander Dilthey, Sergey Koren, Adam M Phillippy   +2 more
exaly   +4 more sources

Completely resolved structural variants by optical genome mapping with adaptive sampling from CNV discovery [PDF]

npj Genomic Medicine
Structural variants (SVs), including duplications, deletions, inversions, translocations, and insertions, play major roles in human phenotypic diversity but remain difficult to detect because of variable size and structural complexity.
Li Fu, Chong Ae Kim, Masatoshi Tokita, Yohane Miyata, Nobuhiko Okamoto, Yoshio Makita, Hitoshi Osaka, Ayataka Fujimoto, Atsuro Daida, Jun Nirei, Noriko Udagawa, Seiichi Hayakawa, Kimiko Deguchi, Mitsumasa Fukuda, Hiroshi Matsumoto, Manami Akasaka, Junichiro Okada, Yohei Misumi, Jun Kido, Toshifumi Suzuki, Hiromi Aoi, Rie Seyama, Haruka Hamanoue, Satomi Mitsuhashi, Sachiko Ohori, Ken Saida, Yuta Inoue, Kohei Hamanaka, Naomi Tsuchida, Yuri Uchiyama, Eriko Koshimizu, Satoko Miyatake, Takeshi Mizuguchi, Atsuo Itakura, Naoki Harada, Atsushi Fujita, Naomichi Matsumoto   +36 more
doaj   +2 more sources