Results 31 to 40 of about 283,388 (253)

SHRiMP: accurate mapping of short color-space reads.

PLoS Computational Biology, 2009
The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP
Stephen M Rumble, Phil Lacroute, Adrian V Dalca, Marc Fiume, Arend Sidow, Michael Brudno   +5 more
doaj   +1 more source

hAssembler: A hybrid de novo genome assembly approach for large genomes

The Indian Journal of Agricultural Sciences, 2020
Genome assembly is a process where large contigs and scaffolds are constructed from raw reads generated by sequencing machines. Based on the size of the generated reads they can be primarily categorized into short reads and long reads.
AMIT KAIRI, PRIYANKA GUHA MAJUMDAR, ATMAKURI RAMAKRISHNA RAO   +2 more
doaj   +1 more source

Short Read Mapping: An Algorithmic Tour [PDF]

Proceedings of the IEEE, 2017
Ultra-high-throughput next-generation sequencing (NGS) technology allows us to determine the sequence of nucleotides of many millions of DNA molecules in parallel. Accompanied by a dramatic reduction in cost since its introduction in 2004, NGS technology has provided a new way of addressing a wide range of biological and biomedical questions, from the ...
Stefan Canzar, Steven L. Salzberg
openaire   +3 more sources

A hybrid short read mapping accelerator [PDF]

BMC Bioinformatics, 2013
The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications.
Yupeng Chen, Bertil Schmidt, Douglas L. Maskell   +2 more
openaire   +3 more sources

Sequenciamento de DNA de nova geração e suas aplicações na genômica de plantas Next generation DNA sequencing and its applications in plant genomics

Ciência Rural, 2010
As plataformas de sequenciamento de nova geração são uma alternativa poderosa para estudos de genômica estrutural e funcional. Na genômica de plantas, os trabalhos com as novas plataformas têm sido destinados ao sequenciamento de transcritos ...
Mayra Costa da Cruz Gallo de Carvalho, Danielle Cristina Gregorio da Silva   +1 more
doaj   +1 more source

ReadDB Provides Efficient Storage for Mapped Short Reads

BMC Bioinformatics, 2011
Background The advent of high-throughput sequencing has enabled sequencing based measurements of cellular function, with an individual measurement potentially consisting of more than 108 reads.
Gifford David K, Rolfe P Alexander
doaj   +1 more source

libgapmis: extending short-read alignments [PDF]

BMC Bioinformatics, 2013
Background: A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy.
Nikolaos Alachiotis 0001, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis   +4 more
openaire   +4 more sources

Methods for Allocating Ambiguous Short-reads [PDF]

Communications in Information and Systems, 2010
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Doron Lipson, Terence P. Speed, Margaret Taub   +2 more
openaire   +2 more sources

Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus

Frontiers in Plant Science
Diplocarpon coronariae is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited.
Sophie Richter, Sophie Richter, Sabine Kind, Thomas Oberhänsli, Michael Schneider, Natalia Nenasheva, Katharina Hoff, Jens Keilwagen, Il-Kweon Yeon, Vincent Philion, Shigeki Moriya, Henryk Flachowsky, Andrea Patocchi, Thomas Wolfgang Wöhner   +13 more
doaj   +1 more source

A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads. [PDF]

PLoS ONE, 2016
DNA methylation is an epigenetic modification critical for normal development and diseases. The determination of genome-wide DNA methylation at single-nucleotide resolution is made possible by sequencing bisulfite treated DNA with next generation high ...
Hong Tran, Xiaowei Wu, Saima Tithi, Ming-an Sun, Hehuang Xie, Liqing Zhang   +5 more
doaj   +1 more source