DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Deng, Jizhong; Huang, Huasheng; Yu, Xiaoli; Jin, Ji; Lin, Weisen; Li, Fagen; Song, Zhijiao; Li, Mei; Gan, Siming
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 8
• Publication Date: 2015-12
• Subjects: Diploid -- Insertion-deletion (InDel) -- Resequencing -- Single nucleotide polymorphism (SNP); Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-015-0790-y
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background Amplicon 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. Results We 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. Conclusions The 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.