Results 21 to 30 of about 152,624 (261)
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
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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.
Inanç Birol +14 more
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Feature-by-feature--evaluating de novo sequence assembly. [PDF]
PLoS ONE, 2012 The whole-genome sequence assembly (WGSA) problem is among one of the most studied problems in computational biology. Despite the availability of a plethora of tools (i.e., assemblers), all claiming to have solved the WGSA problem, little has been done ...
Francesco Vezzi +2 more
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Yet another de novo genome assembler [PDF]
2019 11th International Symposium on Image and Signal Processing and Analysis (ISPA), 2019 Abstract Advances in sequencing technologies have pushed the limits of genome assemblies beyond imagination. The sheer amount of long read data that is being generated enables the assembly for even the largest and most complex organism for which efficient algorithms are needed. We present a new tool, called Ra, for de
Robert Vaser, Mile Sikic
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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
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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
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PLoS ONE, 2020 The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes.
Agnes Scheunert +3 more
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Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data. [PDF]
PLoS ONE, 2013 Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects ...
Aarti Desai +7 more
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Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies [PDF]
PeerJ, 2017 Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality
Cédric Cabau +5 more
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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
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