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. 2022 May 11;23(Suppl 4):361.
doi: 10.1186/s12864-022-08577-7.

B-assembler: a circular bacterial genome assembler

Fengyuan Huang  1   2 , Li Xiao  3 , Min Gao  1   3 , Ethan J Vallely  1 , Kevin Dybvig  2   4 , T Prescott Atkinson  4 , Ken B Waites  5 , Zechen Chong  6   7
Affiliations

B-assembler: a circular bacterial genome assembler

Fengyuan Huang et al. BMC Genomics. .

Abstract

Background: Accurate bacteria genome de novo assembly is fundamental to understand the evolution and pathogenesis of new bacteria species. The advent and popularity of Third-Generation Sequencing (TGS) enables assembly of bacteria genomes at an unprecedented speed. However, most current TGS assemblers were specifically designed for human or other species that do not have a circular genome. Besides, the repetitive DNA fragments in many bacterial genomes plus the high error rate of long sequencing data make it still very challenging to accurately assemble their genomes even with a relatively small genome size. Therefore, there is an urgent need for the development of an optimized method to address these issues.

Results: We developed B-assembler, which is capable of assembling bacterial genomes when there are only long reads or a combination of short and long reads. B-assembler takes advantage of the structural resolving power of long reads and the accuracy of short reads if applicable. It first selects and corrects the ultra-long reads to get an initial contig. Then, it collects the reads overlapping with the ends of the initial contig. This two-round assembling procedure along with optimized error correction enables a high-confidence and circularized genome assembly. Benchmarked on both synthetic and real sequencing data of several species of bacterium, the results show that both long-read-only and hybrid-read modes can accurately assemble circular bacterial genomes free of structural errors and have fewer small errors compared to other assemblers.

Conclusions: B-assembler provides a better solution to bacterial genome assembly, which will facilitate downstream bacterial genome analysis.

Keywords: Bacteria genome; De novo assembly; Hybrid-read assembly; Long-read-only assembly.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The workflow of B-assembler. B-assembler has two modes: long-read-only assembly and hybrid reads assembly
Fig. 2
Fig. 2
Indels and mismatches produced by the benchmarked assemblers on the 14 NCTC PacBio samples. The number of indels and mismatches were added per 100kbp
See this image and copyright information in PMC

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