Results 11 to 20 of about 1,004,545 (280)
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 +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 +7 more
doaj +3 more sources
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 +6 more
europepmc +5 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
Kermit: linkage map guided long read assembly [PDF]
Algorithms for Molecular Biology, 2019 With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs.
Riku Walve, Pasi Rastas, Leena Salmela
openaire +4 more sources
SVIM: structural variant identification using mapped long reads [PDF]
Bioinformatics, 2018 Abstract Motivation Structural variants are defined as genomic variants larger than 50 bp. They have been shown to affect more bases in any given genome than single-nucleotide polymorphisms or small insertions and deletions.
Heller, David, Vingron, Martin
openaire +3 more sources
Epilepsia Open, 2023 Familial adult myoclonic epilepsy (FAME) is an adult‐onset neurological disease characterized by cortical tremor, myoclonus, and seizures due to a pentanucleotide repeat expansion: a combination of pathogenic TTTCA expansion associated with a TTTTA ...
Tatiana Maroilley +8 more
doaj +1 more source
Food Chemistry: Molecular Sciences, 2023 Next-generation-sequencing (NGS) becomes increasingly important for laboratories tasked with the detection of genetically modified organisms (GMOs) in food, feed and seeds.
Steffen Pallarz +4 more
doaj +1 more source
Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. [PDF]
, 2020 Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits.
Andrés, Aida M +7 more
core +3 more sources