Results 31 to 40 of about 6,745,034 (280)

NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads [PDF]

Genomics, Proteomics and Bioinformatics
Shanlin Liu, Depeng Wang, Kai Ye
exaly   +2 more sources

SimLoRD: Simulation of Long Read Data [PDF]

Bioinformatics, 2016
Abstract Motivation: Third generation sequencing methods provide longer reads than second generation methods and have distinct error characteristics. While there exist many read simulators for second generation data, there is a very limited choice for third generation data.
Stöcker, B.K. (Bianca K.), J. Köster (Johannes), S. Rahmann (Sven)   +2 more
openaire   +3 more sources

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Genome Biology, 2022
Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by ...
Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson, Abhinav Nellore   +4 more
doaj   +1 more source

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper [PDF]

, 2018
Abstract Recent advances in long-read sequencing enable the characterization of genome structure and its intra- and inter-species variation at a resolution that was previously impossible. Detecting overlaps between reads is integral to many long-read genomics pipelines, such as de novo
Guidi, Giulia, Ellis, Marquita, Rokhsar, Daniel, Yelick, Katherine, Buluç, Aydın   +4 more
openaire   +3 more sources

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, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve   +3 more
openaire   +3 more sources

HASLR: Fast Hybrid Assembly of Long Reads

iScience, 2020
Summary: Third-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and potentially gap-free assemblies.
Ehsan Haghshenas, Hossein Asghari, Jens Stoye, Cedric Chauve, Faraz Hach   +4 more
doaj   +1 more source

Haplotype-aware diplotyping from noisy long reads

Genome Biology, 2019
Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging ...
Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall, Benedict Paten   +4 more
doaj   +1 more source

Critical length in long-read resequencing [PDF]

NAR Genomics and Bioinformatics, 2019
Abstract Long-read sequencing has substantial advantages for structural variant discovery and phasing of variants compared to short-read technologies, but the required and optimal read length has not been assessed. In this work, we used long reads simulated from human genomes and evaluated structural variant discovery and variant phasing
Wouter, De Coster, Mojca, Strazisar, Peter, De Rijk   +2 more
openaire   +3 more sources

Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome, 2021
Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing.
Benjamin J. Callahan, Dmitry Grinevich, Siddhartha Thakur, Michael A. Balamotis, Tuval Ben Yehezkel   +4 more
doaj   +1 more source

S-conLSH: alignment-free gapped mapping of noisy long reads

BMC Bioinformatics, 2021
Background The advancement of SMRT technology has unfolded new opportunities of genome analysis with its longer read length and low GC bias. Alignment of the reads to their appropriate positions in the respective reference genome is the first but ...
Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay   +2 more
doaj   +1 more source