ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis

被引：42

作者：

He, W. ^{[1
,2
]}

Zhao, S. ^{[2
]}

Liu, X. ^{[2
]}

Dong, S. ^{[2
]}

Lv, J. ^{[2
]}

Liu, D. ^{[2
]}

Wang, J. ^{[1
,2
]}

Meng, Z. ^{[1
]}

机构：

[1] China Univ Technol, Sch Biosci & Bioengn, Guangzhou, Guangdong, Peoples R China

[2] BGI Shenzhen, Shenzhen, Peoples R China

来源：

GENETICS AND MOLECULAR RESEARCH | 2013年 / 12卷 / 04期

关键词：

Next-generation sequencing; Resequencing; Toolkit; Sequence variation; GENOME SEQUENCE; ALIGNMENT;

D O I：

10.4238/2013.December.4.15

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Large-scale next-generation sequencing (NGS)-based resequencing detects sequence variations, constructs evolutionary histories, and identifies phenotype-related genotypes. However, NGS-based resequencing studies generate extraordinarily large amounts of data, making computations difficult. Effective use and analysis of these data for NGS-based resequencing studies remains a difficult task for individual researchers. Here, we introduce ReSeqTools, a full-featured toolkit for NGS (Illumina sequencing)-based resequencing analysis, which processes raw data, interprets mapping results, and identifies and annotates sequence variations. ReSeqTools provides abundant scalable functions for routine resequencing analysis in different modules to facilitate customization of the analysis pipeline. ReSeqTools is designed to use compressed data files as input or output to save storage space and facilitates faster and more computationally efficient large-scale resequencing studies in a user-friendly manner. It offers abundant practical functions and generates useful statistics during the analysis pipeline, which significantly simplifies resequencing analysis. Its integrated algorithms and abundant sub-functions provide a solid foundation for special demands in resequencing projects. Users can combine these functions to construct their own pipelines for other purposes.

引用

页码：6275 / 6283

页数：9

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