Results 1 to 10 of about 225,232 (252)

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

PLoS Comput Biol, 2022
AbstractMotivationSequencing 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 bacteria.
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

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   +3 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

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

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

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

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   +3 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

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.
  +8 more sources