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

BMC Genomics

Software

Wenwei Xiong¹  Chunguang Du¹  Limei He²  Yubin Li²  Hugo K Dooner² 

[1] Department of Biology and Molecular Biology, Montclair State University, 07043, Montclair, NJ, USA;Waksman Institute, Rutgers University, 08854, Piscataway, NJ, USA;

关键词: Next-generation sequencing;    Sequence identification;    Target enrichment;    Multidimensional pooling;   

DOI  :  10.1186/1471-2164-14-679

 received in 2013-05-21, accepted in 2013-10-02,  发布年份 2013

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Xiong et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.