Algorisms used for in silico finishing of bacterial genomes based on short-read assemblage implemented in GenoFinisher, AceFileViewer, and ShortReadManager

In these days, for bacterial genome sequence determination, ultralong reads with homopolymeric troubles are used in combinations with short reads, resulting in genomic sequences with possible incorrect uniformity of repeat sequences. We have been determining complete bacterial genomic sequences based on NGS short reads and Newbler assemblage by utilizing functions implemented in 3 software GenoFinisher, AceFileViewer, and ShortReadManager without conducting additional experiments for gap closing, proving the concept that NGS short reads enclose enough information to determine complete genome sequences. Although some manual in silico tasks are to be conducted, they will ultimately be solved in a single pipeline. In this review, we describe the tools and implemented ideas that have enabled complete sequence determination solely based on short reads, which would be useful for establishing the basis for the future development of a short-read-based assembler that enables complete and accurate genome sequence determination at a lower cost.