Results 21 to 30 of about 296,746 (277)
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
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 +3 more
doaj +1 more source
CoLoRMap: Correcting Long Reads by Mapping short reads [PDF]
Bioinformatics, 2016 Abstract Motivation Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies.
Ehsan Haghshenas +3 more
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Long-read single-molecule maps of the functional methylome [PDF]
Genome Research, 2019 We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs.
Hila Sharim +25 more
openaire +5 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
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.
David Heller, Martin Vingron
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Efficient mapping of accurate long reads in minimizer space with mapquik
Genome Research, 2023 DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (e.g., Pacific Biosciences [PacBio] HiFi) to a reference genome, which poses challenges in terms of accuracy and ...
Bariş Ekim +4 more
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Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions
Plants, 2023 High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors.
Luca Marcolungo +10 more
doaj +1 more source
A comprehensive evaluation of alignment algorithms in the context of RNA-seq. [PDF]
, 2012 Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level.
Friedel, Caroline C. +8 more
core +1 more source