Abstract
BackgroundThe 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.ResultsHere 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.ConclusionsInsertionMapper is proven efficacious for the identification of target-enriched sequences from multidimensional high throughput sequencing data. With adjustable parameters and experiment configurations, this tool can save great computational effort to biologists interested in identifying their sequences of interest within the huge output of modern DNA sequencers. InsertionMapper is freely accessible at https://sourceforge.net/p/insertionmapper and http://bo.csam.montclair.edu/du/insertionmapper.
Highlights
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
We illustrate the use of InsertionMapper with an example from our maize genome project that aims to create a large set of single gene knockouts with a transgenic Ds transposon marked with green fluorescent protein (Dsg). This pipeline tool is applicable to similar situations that require analysis of the tremendous output of short reads produced in Next-generation sequencing (NGS) sequencing experiments of targeted genome sequences
The InsertionMapper pipeline tool was originally designed for the identification of Ds-targeted sequences from NGS data, but should suit most scenarios in which biologists want to identify and map targeted sequences from large multidimensional sample pools using high throughput sequencing technology
Summary
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
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