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B-assembler: a circular bacterial genome assembler.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
      Genome, Bacterial* ; High-Throughput Nucleotide Sequencing*/methods; Bacteria/genetics ; DNA ; Humans ; Sequence Analysis, DNA/methods
    • 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.
      (© 2022. The Author(s).)
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    • Grant Information:
      R35 GM138212 United States GM NIGMS NIH HHS; 1OT3HL147154 United States HL NHLBI NIH HHS; 1R35GM138212 United States GM NIGMS NIH HHS
    • Contributed Indexing:
      Keywords: Bacteria genome; De novo assembly; Hybrid-read assembly; Long-read-only assembly
    • Accession Number:
      9007-49-2 (DNA)
    • Publication Date:
      Date Created: 20220513 Date Completed: 20220519 Latest Revision: 20221109
    • Publication Date:
      20230925
    • Accession Number:
      PMC9092672
    • Accession Number:
      10.1186/s12864-022-08577-7
    • Accession Number:
      35546658