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Published on: February 1, 2013
InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput
Wenwei Xiong1, Limei He, Yubin Li
1Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA. duc@mail.montclair.edu.
BMC Genomics
|October 5, 2013
Summary
InsertionMapper is a new computational tool for analyzing targeted next-generation sequencing (NGS) data from complex pooled samples. This pipeline efficiently identifies specific DNA sequences, saving significant computational effort for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Next-generation sequencing (NGS) enables high-throughput analysis but targeted sequencing from many samples requires specialized tools.
- Multidimensional pooling strategies are used for targeted genome region amplification and sequencing.
- A generalized computational tool for analyzing target-enriched NGS data from multidimensional pools was lacking.
Purpose of the Study:
- To present InsertionMapper, a novel pipeline tool for identifying targeted sequences from multidimensional high-throughput sequencing data.
- To provide a generalized solution for the computational analysis of target-enriched NGS data.
Main Methods:
- InsertionMapper comprises four modules: Data Preprocessing, Database Modeling, Dimension Deconvolution, and Element Mapping.
- The tool was illustrated using a project involving sequencing 15,000 transposon insertion sites in maize.
- Identified sequences were validated using PCR assays.
Main Results:
- InsertionMapper effectively identifies targeted sequences from multidimensional high-throughput sequencing data.
- The pipeline tool is applicable to scenarios involving analysis of large outputs of short reads from targeted NGS experiments.
- Demonstrated efficacy in a large-scale maize transposon insertion site sequencing project.
Conclusions:
- InsertionMapper is an efficacious tool for identifying target-enriched sequences in complex NGS datasets.
- The tool offers adjustable parameters and configurations to reduce computational burden for biologists.
- InsertionMapper is freely accessible online for use in identifying specific DNA sequences from large sequencing outputs.
