Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline.
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline.
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DOI：
10.1186/1471-2105-11-269
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发表时间：
2010-05-20
影响因子：
3
通讯作者：
Van Criekinge W
中科院分区：
文献类型：
--
作者：
De Schrijver JM;De Leeneer K;Lefever S;Sabbe N;Pattyn F;Van Nieuwerburgh F;Coucke P;Deforce D;Vandesompele J;Bekaert S;Hellemans J;Van Criekinge W
下一代扩增子测序可实现高通量的基因诊断，在一次测序中对几个患者的多个基因进行测序。目前，还没有开源的开箱即用的软件解决方案，可以可靠地报告检测到的基因变异，并可以通过分析PCR反应来提高未来的测序效率。我们使用Perl和关系数据库开发了一个面向数据库的软件流水线，用于分析454/Roche GS-FLX扩增子重测序实验。该管道实现了变异检测、变异检测验证和高级数据分析，提供了可用于使用传统方法优化PCR效率的信息。模块化方法允许在需要的地方定制管道，并允许研究人员将他们的分析管道应用到他们的实验中。在对实际测序数据使用管道之前，有清晰的文档和培训数据可用于测试和验证管道。我们设计了一个面向开源数据库的管道，可以使用SQL语句对454/Roche GS-Flx扩增子重测序实验进行高级分析。这种模块化的数据库方法可以很容易地与其他管道模块相结合，如变式解释或LIMS系统。还有一套标准的报告脚本可用。
Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions. We developed an integrated database oriented software pipeline for analysis of 454/Roche GS-FLX amplicon resequencing experiments using Perl and a relational database. The pipeline enables variation detection, variation detection validation, and advanced data analysis, which provides information that can be used to optimize PCR efficiency using traditional means. The modular approach enables customization of the pipeline where needed and allows researchers to adopt their analysis pipeline to their experiments. Clear documentation and training data is available to test and validate the pipeline prior to using it on real sequencing data. We designed an open-source database oriented pipeline that enables advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is also a set of standard reporting scripts available.
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影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
影响因子：
12.3
作者：
Flicek P
通讯作者：
Flicek P
亚洲个体的二倍体基因组序列
影响因子：
64.8
作者：
Wang, Jun;Wang, Wei;Li, Ruiqiang;Li, Yingrui;Tian, Geng;Goodman, Laurie;Fan, Wei;Zhang, Junqing;Li, Jun;Zhang, Juanbin;Guo, Yiran;Feng, Binxiao;Li, Heng;Lu, Yao;Fang, Xiaodong;Liang, Huiqing;Du, Zhenglin;Li, Dong;Zhao, Yiqing;Hu, Yujie;Yang, Zhenzhen;Zheng, Hancheng;Hellmann, Ines;Inouye, Michael;Pool, John;Yi, Xin;Zhao, Jing;Duan, Jinjie;Zhou, Yan;Qin, Junjie;Ma, Lijia;Li, Guoqing;Yang, Zhentao;Zhang, Guojie;Yang, Bin;Yu, Chang;Liang, Fang;Li, Wenjie;Li, Shaochuan;Li, Dawei;Ni, Peixiang;Ruan, Jue;Li, Qibin;Zhu, Hongmei;Liu, Dongyuan;Lu, Zhike;Li, Ning;Guo, Guangwu;Zhang, Jianguo;Ye, Jia;Fang, Lin;Hao, Qin;Chen, Quan;Liang, Yu;Su, Yeyang;San, A.;Ping, Cuo;Yang, Shuang;Chen, Fang;Li, Li;Zhou, Ke;Zheng, Hongkun;Ren, Yuanyuan;Yang, Ling;Gao, Yang;Yang, Guohua;Li, Zhuo;Feng, Xiaoli;Kristiansen, Karsten;Wong, Gane Ka-Shu;Nielsen, Rasmus;Durbin, Richard;Bolund, Lars;Zhang, Xiuqing;Li, Songgang;Yang, Huanming;Wang, Jian
通讯作者：
Wang, Jian
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL
DOI：
10.1093/bioinformatics/btp698
发表时间：
2010-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Durbin R
通讯作者：
Durbin R