Platanus-B: An accurate de novo assembler for bacterial genomes using an iterative error-removal process

Rei Kajitani, Dai Yoshimura, Yoshitoshi Ogura, Yasuhiro Gotoh, Tetsuya Hayashi, Takehiko Itoh

研究成果: ジャーナルへの寄稿学術誌査読

25 被引用数 (Scopus)

抄録

De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus-B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus-B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus-B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus-B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.

本文言語英語
論文番号dsaa014
ジャーナルDNA Research
27
3
DOI
出版ステータス出版済み - 6月 1 2020

!!!All Science Journal Classification (ASJC) codes

  • 分子生物学
  • 遺伝学

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