文献类型：期刊文献

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

作者：Deng, Jizhong[1] Huang, Huasheng[1,3] Yu, Xiaoli[2,4] Jin, Ji[1] Lin, Weisen[1] Li, Fagen[4] Song, Zhijiao[4] Li, Mei[4] Gan, Siming[2,4]

第一作者：Deng, Jizhong

通信作者：Gan, SM[1]

机构：[1]South China Agr Univ, Coll Engn, Guangzhou 510642, Guangdong, Peoples R China;[2]Chinese Acad Forestry, State Key Lab Tree Genet & Breeding, Beijing 100091, Peoples R China;[3]Guangdong Univ Sci & Technol, Dept Comp Sci, Dongguan 523083, Peoples R China;[4]Chinese Acad Forestry, Res Inst Trop Forestry, Guangzhou 510520, Guangdong, Peoples R China

年份：2015

卷号：16

期号：1

外文期刊名：BMC BIOINFORMATICS

收录：;EI(收录号：20154401463863);Scopus(收录号：2-s2.0-84945137827);WOS:【SCI-EXPANDED(收录号:WOS:000363374500003)】；

基金：This work was supported by the Ministry of Science and Technology of China (2012CB114505, 2011AA100202) and the National Natural Science Foundation of China (31270702, 31070592). We thank Youpei Cao for provision of the scf sequencing files.

语种：英文

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

摘要：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.