scholarly journals A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

PLoS ONE ◽  
2011 ◽  
Vol 6 (3) ◽  
pp. e17915 ◽  
Author(s):  
Wenyu Zhang ◽  
Jiajia Chen ◽  
Yang Yang ◽  
Yifei Tang ◽  
Jing Shang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Software Tools ◽  
Next Generation ◽  
De Novo Genome Assembly ◽  
Sequencing Technologies ◽  
Generation Sequencing ◽  
Assembly Software

scholarly journals Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework

BMC Genomics ◽  
2015 ◽  
Vol 16 (Suppl 12) ◽  
pp. S9 ◽  
Author(s):  
Chih-Hao Fang ◽  
Yu-Jung Chang ◽  
Wei-Chun Chung ◽  
Ping-Heng Hsieh ◽  
Chung-Yen Lin ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Subset Selection ◽  
Next Generation ◽  
Mapreduce Framework ◽  
De Novo Genome Assembly ◽  
Generation Sequencing ◽  
High Depth ◽  
Selection Of

scholarly journals Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e62856 ◽  
Author(s):  
Yen-Chun Chen ◽  
Tsunglin Liu ◽  
Chun-Hui Yu ◽  
Tzen-Yuh Chiang ◽  
Chi-Chuan Hwang
Keyword(s):  
Next Generation Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
De Novo Genome Assembly ◽  
Gc Bias ◽  
Generation Sequencing

Next generation sequencing under de novo genome assembly

2015 ◽  
Vol 08 (05) ◽  
pp. 1530001 ◽  
Author(s):  
Sonia Farhana Nimmy ◽  
M. S. Kamal
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
De Novo ◽  
Vital Role ◽  
De Bruijn Graph ◽  
Mathematical Tool ◽  
Next Generation ◽  
De Novo Genome Assembly ◽  
Software Packages ◽  
Generation Sequencing

The next generation sequencing (NGS) is an important process which assures inexpensive organization of vast size of raw sequence dataset over any traditional sequencing systems or methods. Various aspects of NGS such as template preparation, sequencing imaging and genome alignment and assembly outline the genome sequencing and alignment. Consequently, de Bruijn graph (dBG) is an important mathematical tool that graphically analyzes how the orientations are constructed in groups of nucleotides. Basically, dBG describes the formation of the genome segments in circular iterative fashions. Some pivotal dBG-based de novo algorithms and software packages such as T-IDBA, Oases, IDBA-tran, Euler, Velvet, ABySS, AllPaths, SOAPde novo and SOAPde novo2 are illustrated in this paper. Consequently, overlap layout consensus (OLC) graph-based algorithms also play vital role in NGS assembly. Some important OLC-based algorithms such as MIRA3, CABOG, Newbler, Edena, Mosaik and SHORTY are portrayed in this paper. It has been experimented that greedy graph-based algorithms and software packages are also vital for proper genome dataset assembly. A few algorithms named SSAKE, SHARCGS and VCAKE help to perform proper genome sequencing.

scholarly journals Comparative studies of de novo assembly tools for next-generation sequencing technologies

2011 ◽  
Vol 27 (15) ◽  
pp. 2031-2037 ◽  
Author(s):  
Yong Lin ◽  
Jian Li ◽  
Hui Shen ◽  
Lei Zhang ◽  
Christopher J. Papasian ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Comparative Studies ◽  
De Novo Assembly ◽  
De Novo ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Generation Sequencing
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