Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Toward Complete Bacterial Genome Sequencing Through the Combined Use of Multiple Next-Generation Sequencing Platforms

  • Jeong, Haeyoung (Super-Bacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Lee, Dae-Hee (Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Ryu, Choong-Min (Super-Bacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Park, Seung-Hwan (Super-Bacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB))
  • Received : 2015.07.15
  • Accepted : 2015.10.14
  • Published : 2016.01.28
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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 second-generation, 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.

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