title: Toward Complete Bacterial Genome Sequencing Through the Combined Use of Multiple Next-Generation Sequencing Platforms.
abstract: PacBio's long-read sequencing technologies can be successfully used for a complete bacterial genome assembly using recently developed non-hybrid assemblers in the absence of secondgeneration, high-quality short reads. However, standardized procedures that take into account multiple pre-existing second-generation sequencing platforms are scarce. In addition to Illumina HiSeq and Ion Torrent PGM-based genome sequencing results derived from previous studies, we generated further sequencing data, including from the PacBio RS II platform, and applied various bioinformatics tools to obtain complete genome assemblies for five bacterial strains. Our approach revealed that the hierarchical genome assembly process (HGAP) non-hybrid assembler resulted in nearly complete assemblies at a moderate coverage of ~75x, but that different versions produced non-compatible results requiring post processing. The other two platforms further improved the PacBio assembly through scaffolding and a final error correction.
authors.affiliation: Super-Bacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.|Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea.
authors.forename: Haeyoung
authors.initials: H
authors.lastname: Jeong
authors.affiliation: Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.|Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea.
authors.forename: Dae-Hee
authors.initials: DH
authors.lastname: Lee
authors.affiliation: Super-Bacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.|Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea.
authors.forename: Choong-Min
authors.initials: CM
authors.lastname: Ryu
authors.affiliation: Super-Bacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.|Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea.
authors.forename: Seung-Hwan
authors.initials: SH
authors.lastname: Park
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D012984:Software
keywords: PacBio; complete genome sequencing; next-generation sequencing; non-hybrid assembly