InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data

BMC Genomics
Wenwei XiongChunguang Du


The advent of next-generation high-throughput technologies has revolutionized whole genome sequencing, yet some experiments require sequencing only of targeted regions of the genome from a very large number of samples. These regions can be amplified by PCR and sequenced by next-generation methods using a multidimensional pooling strategy. However, there is at present no available generalized tool for the computational analysis of target-enriched NGS data from multidimensional pools. Here we present InsertionMapper, a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. InsertionMapper consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. We illustrate InsertionMapper with an example from our project 'New reverse genetics resources for maize', which aims to sequence-index a collection of 15,000 independent insertion sites of the transposon Ds in maize. Identified sequences are validated by PCR assays. This pipeline tool is applicable to similar scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. InsertionMap...Continue Reading


Oct 4, 2015·Nucleic Acids Research·Carson M AndorfCarolyn J Lawrence-Dill
Apr 18, 2019·Proceedings of the National Academy of Sciences of the United States of America·Hugo K DoonerChunguang Du


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