Results 21 to 30 of about 334,258 (285)
Challenges and advances for transcriptome assembly in non-model species. [PDF]
PLoS ONE, 2017 Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly.
Arnaud Ungaro +6 more
doaj +1 more source
Comparative analysis of de novo transcriptome assembly [PDF]
Science China Life Sciences, 2013 The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq
Clarke, Kaitlin +4 more
openaire +2 more sources
De novo assembly of short sequence reads [PDF]
Briefings in Bioinformatics, 2010 A new generation of sequencing technologies is revolutionizing molecular biology. Illumina's Solexa and Applied Biosystems' SOLiD generate gigabases of nucleotide sequence per week. However, a perceived limitation of these ultra-high-throughput technologies is their short read-lengths.
Konrad, Paszkiewicz, David J, Studholme
openaire +2 more sources
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly [PDF]
, 2012 Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly.
Depristo +15 more
core +1 more source
G3: Genes, Genomes, Genetics, 2016 The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes.
Xiaofan Zhou +5 more
doaj +1 more source
De novo transcriptome assembly with ABySS [PDF]
Bioinformatics, 2009 Abstract Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts.
Birol, I. +14 more
openaire +3 more sources
Faucet: streaming de novo assembly graph construction [PDF]
Bioinformatics, 2017 AbstractMotivationWe present Faucet, a 2-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded.
Rozov, Roye +3 more
openaire +2 more sources
De Novo Repeat Classification and Fragment Assembly [PDF]
Genome Research, 2004 Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats.
Pavel A, Pevzner +3 more
openaire +2 more sources
A consensus-based ensemble approach to improve transcriptome assembly
BMC Bioinformatics, 2021 Background Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome.
Adam Voshall +8 more
doaj +1 more source
Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly
BMC Genomics, 2018 Background De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera ‘Sultanina’ genome assemblies for comparison with the inbred V. vinifera (
Sagar Patel +5 more
doaj +1 more source