Results 21 to 30 of about 59,976,998 (309)

Hardware acceleration of de novo genome assembly [PDF]

International Journal of Embedded Systems, 2017
The cost of genome assembly has gone down drastically with the advent of next generation sequencing technologies. These new sequencing technologies produce large amounts of DNA fragments. Software programs are used to construct the genome from these DNA fragments. The assembly programs take significant amount of time to execute. To reduce the execution
Varma, Sharat Chandra, Kolin, Paul, Balakrishnan, M., Lavenier, Dominique   +3 more
openaire   +2 more sources

In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

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, David Peris, Jacek Kominek, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas   +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.
Inanç Birol, Shaun D. Jackman, Cydney B. Nielsen, Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao 0002, Martin Hirst, Jacqueline E. Schein, Douglas E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Steven J. M. Jones   +14 more
openaire   +4 more sources

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis [PDF]

, 2010
Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing.
Kück Ulrich, Espagne, Eric, Jason E Stajich, Kempken, Frank, Ines Engh, Stefanie Pöggeler, Frank Kempken, Ulrich Kück, Kuo, Hsiao Che, Jens Kamerewerd, Osiewacz, Heinz D., Zickler, Denise, Espagne Eric, Kück, Ulrich, Engh Ines, Freitag, Michael H., Smith, Kristina M, Meiling Chu, Chu Meiling, Smith Kristina M., Kuo, Hsiao-Che, Read, Nick D, Heinz D Osiewacz, Kempken Frank, Poeggeler, Stefanie, Knab, Birgit, Birgit Knab, Denise Zickler, Kuo Hsiao-Che, Kueck, Ulrich, Stajich Jason E., Osiewacz, Heinz D, Stajich, Jason E, Michael Freitag, Stephan Seiler, Halliday, Karen, Freitag, Michael, Stajich, Jason E., Chu, Meiling, Nick D Read, Karen Halliday, Knab Birgit, Zickler Denise, Kristina M Smith, Pöggeler, Stefanie, Engh, Ines, Eric Espagne, Hsiao-Che Kuo, Kamerewerd Jens, Smith, Kristina M., Halliday Karen, Pöggeler Stefanie, Seiler Stephan, Read Nick D., Nowrousian, Minou, Seiler, Stephan, Osiewacz Heinz D., Freitag Michael, Nowrousian Minou, Read, Nick D., Kamerewerd, Jens, Minou Nowrousian   +61 more
core   +2 more sources

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, Giuseppe Narzisi, Bud Mishra   +2 more
doaj   +1 more source

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
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, Sairam Behera, Xiangjun Li, Xiao-Hong Yu, Kushagra Kapil, Jitender S. Deogun, John Shanklin, Edgar B. Cahoon, Etsuko N. Moriyama   +8 more
doaj   +1 more source

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies [PDF]

, 2014
Background: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O.
Moreau, Hervé, Van De Peer, Yves, Adam Eyre-Walker, Château, Annie, Van de Peer, Y., Stephane Rombauts, Carré, Isabelle, Eyre-Walker, Adam, Rivals, E., Peer, Yves van de, Wendy Schackwitz, Schackwitz, Wendy, Benoit Piégu, Moreau, H., Schackwitz, W., Grimsley, Nigel, Evelyne Derelle, Rombauts, Stephane, Eyre Walker, Adam, Blanc-Mathieu, R., Eyre-Walker, A., Verhelst, B., Blanc-Mathieu, Romain, Bouget, François-Yves, Hervé Moreau, Nigel Grimsley, Rivals, Eric, Piégu, Benoit, Isabelle Carré, François-Yves Bouget, Derelle, Evelyne, Eric Rivals, Carré, I., Gwenaël Piganeau, Derelle, E., Bram Verhelst, Verhelst, Bram, Annie Château, Romain Blanc-Mathieu, Bouget, F.-Y., Château, A., Carré, Isabelle A., Piégu, B., Grimsley, N., Piganeau, G., Rombauts, S., Piganeau, Gwenaël, Blanc Mathieu, Romain, Yves Van de Peer   +48 more
core   +1 more source

Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing.

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, Marco Dorfner, Thomas Lingl, Christoph Oberprieler   +3 more
doaj   +1 more source

NCGAS/de-novo-transcriptome-assembly-pipeline: Generating a DOI

, 2020
National Center for Genome Analysis Support (NCGAS) de novo transcriptome assembly ...
Ganote, Carrie, Sanders, Sheri, Papudeshi, Bhavya   +2 more
core   +1 more source