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http://dx.doi.org/10.5808/GI.2017.15.4.128

misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny  

Ko, Young-Joon (Department of Bioinformatics and Life Science, Soongsil University)
Kim, Jung Sun (Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration)
Kim, Sangsoo (Department of Bioinformatics and Life Science, Soongsil University)
Publication Information
Genomics & Informatics / v.15, no.4, 2017 , pp. 128-135 More about this Journal
Abstract
As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.
Keywords
BAC end library; gene synteny; genotyping-by-sequencing; miassembly; next-generation sequencing; reference genome;
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