DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid.
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.
College of Engineering, South China Agricultural University, Wushan Road, Guangzhou, 510642, China. jz-deng@scau.edu.cn.
Jizhong
J
Deng
College of Engineering, South China Agricultural University, Wushan Road, Guangzhou, 510642, China. huanghsheng@126.com.|Department of Computer Science, Guangdong University of Science and Technology, Xihu Road, Dongguan, 523083, China. huanghsheng@126.com.
Huasheng
H
Huang
State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China. zouxiaqu99@163.com.|Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China. zouxiaqu99@163.com.
Xiaoli
X
Yu
College of Engineering, South China Agricultural University, Wushan Road, Guangzhou, 510642, China. ji_king314@aliyun.com.
Ji
J
Jin
College of Engineering, South China Agricultural University, Wushan Road, Guangzhou, 510642, China. 576920627@qq.com.
Weisen
W
Lin
Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China. lifagen2002@126.com.
Fagen
F
Li
Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China. 277856054@qq.com.
Zhijiao
Z
Song
Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China. limei3043@126.com.
Mei
M
Li
State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China. Siming_Gan@126.com.|Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China. Siming_Gan@126.com.
Siming
S
Gan
D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004171:Diploidy; D020224:Expressed Sequence Tags; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software
D004247:DNA