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DOI10.1142/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
ISSN1793-5245
EISSN1793-7159
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
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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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