Results 1 to 10 of about 111,403 (262)

Empirical evaluation of methods for de novo genome assembly [PDF]

PeerJ Computer Science, 2021
Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms.
Firaol Dida, Gangman Yi
doaj   +4 more sources

Linear time complexity de novo long read genome assembly with GoldRush

Nature Communications, 2023
Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap – its most costly step – was improved in modern long read genome assemblers, these tools still often require excessive ...
Johnathan Wong, Lauren Coombe, Vladimir Nikolić, Emily Zhang, Ka Ming Nip, Puneet Sidhu, René L. Warren, Inanç Birol   +7 more
doaj   +2 more sources

Graph Theoretical Strategies in De Novo Assembly

IEEE Access, 2022
De novo genome assemblers assume the reference genome is unavailable, incomplete, highly fragmented, or significantly altered as in cancer tissues. Algorithms for de novo assembly have been developed to deal with and assemble a large number of short ...
Kimia Behizadi, Nafiseh Jafarzadeh, Ali Iranmanesh   +2 more
doaj   +1 more source

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

Genome assembly using quantum and quantum-inspired annealing

Scientific Reports, 2021
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine.
A. S. Boev, A. S. Rakitko, S. R. Usmanov, A. N. Kobzeva, I. V. Popov, V. V. Ilinsky, E. O. Kiktenko, A. K. Fedorov   +7 more
doaj   +1 more source

Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual

G3: Genes, Genomes, Genetics, 2020
In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome, in which ...
llya Soifer, Nicole L. Fong, Nelda Yi, Andrea T. Ireland, Irene Lam, Matthew Sooknah, Jonathan S. Paw, Paul Peluso, Gregory T. Concepcion, David Rank, Alex R. Hastie, Vladimir Jojic, J. Graham Ruby, David Botstein, Margaret A. Roy   +14 more
doaj   +1 more source

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, Veer Singh Marwah, Akshay Yadav, Vineet Jha, Kishor Dhaygude, Ujwala Bangar, Vivek Kulkarni, Abhay Jere   +7 more
doaj   +1 more source

Efficient assembly of nanopore reads via highly accurate and intact error correction

Nature Communications, 2021
Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore ...
Ying Chen, Fan Nie, Shang-Qian Xie, Ying-Feng Zheng, Qi Dai, Thomas Bray, Yao-Xin Wang, Jian-Feng Xing, Zhi-Jian Huang, De-Peng Wang, Li-Juan He, Feng Luo, Jian-Xin Wang, Yi-Zhi Liu, Chuan-Le Xiao   +14 more
doaj   +1 more source

NSIT: novel sequence identification tool. [PDF]

PLoS ONE, 2014
Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths.
Benjarath Pupacdi, Asif Javed, Mohammed J Zaki, Mathuros Ruchirawat   +3 more
doaj   +1 more source

Reference-guided de novo assembly approach improves genome reconstruction for related species

BMC Bioinformatics, 2017
Background The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions ...
Heidi E. L. Lischer, Kentaro K. Shimizu
doaj   +1 more source