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

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 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 and . We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.