Comparisons of several softwares to detect medium- and large-sized deletions based on next generation sequencing data

Yao Wen; Xie Weibo

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Comparisons of several softwares to detect medium- and large-sized deletions based on next generation sequencing data

Yao Wen,Xie Weibo * #

National Center of Plant Gene Research (Wuhan), National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

*Correspondence author

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Funding: This work was supported by grants from the Research Fund for the Doctoral Program of Higher Education of China （No.Grant No. 20110146120013)）

Opened online: 2 December 2015

Accepted by: none

Citation: Yao Wen,Xie Weibo.Comparisons of several softwares to detect medium- and large-sized deletions based on next generation sequencing data[OL]. [ 2 December 2015] http://en.paper.edu.cn/en_releasepaper/content/4664949

Next generation sequencing (NGS) technologies have enabled us to detect sequence variations effectively. And there are many softwares developed to facilitate and simplify this task. In this study, we carry out detailed comparisons between BreakDancer, Pindel, CNV-seq, CNVnator, inGAP-sv and Defind using both simulation data and real data to detect medium- and large-sized deletions. Defind and CNVnator are the only two methods capable of detecting the completed deletion of Ghd7 in the rice cultivar Zhenshan 97 and Defind performs robustly at different sequence coverage with different read length in the simulation study. The results demonstrate the advantage of combining different types of signature in NGS data to identify deletions. Our studies also provided a significant practical guidance to select appropriate methods to detect medium- and large-sized genomic deletions using NGS data.

Keywords:bioinformatics; genomic deletion; next generation sequencing; software

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