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

BMC Genomics
Wenwei XiongChunguang Du

Abstract

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

References

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

Citations

Aug 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·R R ZwaalR H Plasterk
Mar 23, 2002·The Plant Cell·Matthew CowperthwaiteHugo K Dooner
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Huihua Fu, Hugo K Dooner
Jan 1, 1951·Cold Spring Harbor Symposia on Quantitative Biology·B McCLINTOCK
Feb 12, 2008·Trends in Genetics : TIG·Elaine R Mardis
Mar 19, 2008·The Plant Journal : for Cell and Molecular Biology·Michiel VandenbusscheTom Gerats
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
Jan 30, 2010·Nature Methods·Lira MamanovaDaniel J Turner
Jun 29, 2010·The Plant Cell·Erik VollbrechtThomas P Brutnell
Oct 19, 2010·Nature Methods·Isaäc J NijmanEdwin Cuppen
Jun 1, 2011·Database : the Journal of Biological Databases and Curation·Mary L SchaefferCarolyn J Lawrence
Dec 3, 2011·BMC Genomics·Chunguang DuHugo K Dooner
Aug 7, 2013·Methods in Molecular Biology·Yubin LiHugo K Dooner

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