DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid

BMC Bioinformatics

Software

Ji Jin¹  Jizhong Deng¹  Weisen Lin¹  Huasheng Huang²  Zhijiao Song³  Mei Li³  Fagen Li³  Xiaoli Yu⁴  Siming Gan⁴ 

[1] College of Engineering, South China Agricultural University, Wushan Road, 510642, Guangzhou, China;College of Engineering, South China Agricultural University, Wushan Road, 510642, Guangzhou, China;Department of Computer Science, Guangdong University of Science and Technology, Xihu Road, 523083, Dongguan, China;Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, 510520, Guangzhou, China;State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, 100091, Beijing, China;Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, 510520, Guangzhou, China;

关键词: Diploid;    Insertion-deletion (InDel);    Resequencing;    Single nucleotide polymorphism (SNP);   

DOI  :  10.1186/s12859-015-0790-y

 received in 2015-04-07, accepted in 2015-10-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundAmplicon re-sequencing based on the automated Sanger method remains popular for detection of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels) for a spectrum of genetics applications. However, existing software tools for detecting intra-individual SNPs and InDels in direct amplicon sequencing of diploid samples are insufficient in analyzing single traces and their accuracy is still limited.ResultsWe developed a novel computation tool, named DiSNPindel, to improve the detection of intra-individual SNPs and InDels in direct amplicon sequencing of a diploid. Neither reference sequence nor additional sample was required. Using two real datasets, we demonstrated the usefulness of DiSNPindel in its ability to improve largely the true SNP and InDel discovery rates and reduce largely the missed and false positive rates as compared with existing detection methods.ConclusionsThe software DiSNPindel presented here provides an efficient tool for intra-individual SNP and InDel detection in diploid amplicon sequencing. It will also be useful for identification of DNA variations in expressed sequence tag (EST) re-sequencing.

【 授权许可】

CC BY   
© Deng et al. 2015