Results 21 to 30 of about 1,004,545 (280)

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, S Cenk, Sahinalp, Cedric, Chauve   +3 more
openaire   +2 more sources

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, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato, Massimo Delledonne   +10 more
doaj   +1 more source

ACCURATE LONG READ MAPPING USING ENHANCED SUFFIX ARRAYS [PDF]

Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, 2011
With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs.
Vyverman, Michaël, De Schrijver, Joachim, Van Criekinge, Wim, Dawyndt, Peter, Fack, Veerle   +4 more
openaire   +3 more sources

Jabba: hybrid error correction for long sequencing reads using maximal exact matches [PDF]

, 2015
Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged
Audenaert, P., Demeester, Piet, Fostier, Jan, Heydari, Mahdi, Miclotte, Giles   +4 more
core   +1 more source

Merging short and stranded long reads improves transcript assembly.

PLoS Computational Biology, 2023
Long-read RNA sequencing has arisen as a counterpart to short-read sequencing, with the potential to capture full-length isoforms, albeit at the cost of lower depth.
Amoldeep S Kainth, Gabriela A Haddad, Johnathon M Hall, Alexander J Ruthenburg   +3 more
doaj   +1 more source

The hidden perils of read mapping as a quality assessment tool in genome sequencing [PDF]

, 2017
This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are ...
A Bankevich, AV Karlyshev, D Antipov, EW Myers, HC Lin, IJ Tsai, J Parkhill, K Rutherford, M Hunt, M Land, MT Swain, S Lin, S Meader, TD Otto, TJ Carver   +14 more
core   +1 more source

kngMap: Sensitive and Fast Mapping Algorithm for Noisy Long Reads Based on the K-Mer Neighborhood Graph

Frontiers in Genetics, 2022
With the rapid development of single molecular sequencing (SMS) technologies such as PacBio single-molecule real-time and Oxford Nanopore sequencing, the output read length is continuously increasing, which has dramatical potentials on cutting-edge ...
Ze-Gang Wei, Xing-Guo Fan, Hao Zhang, Xiao-Dan Zhang, Fei Liu, Yu Qian, Shao-Wu Zhang   +6 more
doaj   +1 more source

Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing [PDF]

, 2017
Compared with conventional methods, single-molecule real-time (SMRT) DNA sequencing exhibits longer read lengths than conventional methods, less GC bias, and the ability to read DNA base modifications.
Henley, Robert Y., Jadhav, Vivek, Korlach, Jonas, Larkin, Joseph, Wanunu, Meni   +4 more
core   +1 more source

smsMap: mapping single molecule sequencing reads by locating the alignment starting positions

BMC Bioinformatics, 2020
Background Single Molecule Sequencing (SMS) technology can produce longer reads with higher sequencing error rate. Mapping these reads to a reference genome is often the most fundamental and computing-intensive step for downstream analysis. Most existing
Ze-Gang Wei, Shao-Wu Zhang, Fei Liu
doaj   +1 more source

Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics [PDF]

, 2015
Next Generation Sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For
Cannon, Charles H., Deng, Minghua, Reinert, Gesine, Ren, Jie, Song, Kai, Sun, Fengzhu   +5 more
core   +1 more source