Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0790-y) contains supplementary material, which is available to authorized users.
Highlights
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
In this paper we present a novel computational tool that enables automatic detection of intra-individual SNPs and InDels in direct amplicon sequencing of a diploid sample needless of a reference sequence
Intra-individual SNP diagnosis Totally 110 iterations were performed for LM-Back-propagation neural networks (BPNN) training
Summary
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. Single nucleotide polymorphisms (SNPs) and insertiondeletion polymorphisms (InDels) have become the most commonly used DNA markers because they are codominant, abundant within the genome and amenable to flexible genotyping techniques [1, 2] They could be derived from a number of sources, including re-sequenced polymerase chain reaction (PCR) amplicons, genomic libraries and expressed sequence tag (EST) datasets [3]. Genomic and EST resources, in large scale in particular, tend to be produced with the aid of next-generation sequencing (NGS), amplicon resequencing based on the automated Sanger method remains popular for a spectrum of genetics applications. Direct sequencing involves generally both strands (alleles) of a diploid, and double peaks will
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