Knowledge Resource Center for Ecological Environment in Arid Area
DOI | 10.1142/S1793524515300018 |
Next generation sequencing under de novo genome assembly | |
Nimmy, Sonia Farhana; Kamal, M. S. | |
通讯作者 | Nimmy, Sonia Farhana |
来源期刊 | INTERNATIONAL JOURNAL OF BIOMATHEMATICS
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ISSN | 1793-5245 |
EISSN | 1793-7159 |
出版年 | 2015 |
卷号 | 8期号:5 |
英文摘要 | 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. |
英文关键词 | Next generation sequencing (NGS) short read sequence (SRS) de Bruijn graph (dBG) SOAP denovo2 overlap layout consensus |
类型 | Review |
语种 | 英语 |
国家 | Bangladesh |
收录类别 | SCI-E |
WOS记录号 | WOS:000359722000001 |
WOS关键词 | SHORT DNA-SEQUENCES ; RNA-SEQ ; SHORT READS ; ALGORITHM ; MILLIONS ; ARACHNE ; VELVET ; CELL |
WOS类目 | Mathematical & Computational Biology |
WOS研究方向 | Mathematical & Computational Biology |
资源类型 | 期刊论文 |
条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/187938 |
作者单位 | BGC Trust Univ, Dept Comp Sci & Engn, Chandanaish, Chittagong, Bangladesh |
推荐引用方式 GB/T 7714 | Nimmy, Sonia Farhana,Kamal, M. S.. Next generation sequencing under de novo genome assembly[J],2015,8(5). |
APA | Nimmy, Sonia Farhana,&Kamal, M. S..(2015).Next generation sequencing under de novo genome assembly.INTERNATIONAL JOURNAL OF BIOMATHEMATICS,8(5). |
MLA | Nimmy, Sonia Farhana,et al."Next generation sequencing under de novo genome assembly".INTERNATIONAL JOURNAL OF BIOMATHEMATICS 8.5(2015). |
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