1887

Abstract

Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. The chewBBACA software uses Python 3.4 or higher and can run on a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA.

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/content/journal/mgen/10.1099/mgen.0.000166
2018-03-15
2021-10-19
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References

  1. Lynch T, Petkau A, Knox N, Graham M, van Domselaar G et al. A primer on infectious disease bacterial genomics. Clin Microbiol Rev 2016; 29:881–913 [View Article][PubMed]
    [Google Scholar]
  2. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 1998; 95:3140–3145 [View Article][PubMed]
    [Google Scholar]
  3. Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I et al. PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill 2017; 22:13–24 [View Article][PubMed]
    [Google Scholar]
  4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ et al. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  5. Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes . Nat Microbiol 2016; 2:16185 [View Article][PubMed]
    [Google Scholar]
  6. Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL et al. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Listeria monocytogenes . J Clin Microbiol 2015; 53:2869–2876 [View Article][PubMed]
    [Google Scholar]
  7. Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11:595 [View Article][PubMed]
    [Google Scholar]
  8. Zhang J, Halkilahti J, Hänninen ML, Rossi M. Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy. J Clin Microbiol 2015; 53:1765–1767 [View Article][PubMed]
    [Google Scholar]
  9. Feijão P, Yao HT, Fornika D, Gardy J, Hsiao W et al. MentaLiST – A fast MLST caller for large MLST schemes. Microb Genom 2018 [View Article][PubMed]
    [Google Scholar]
  10. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article][PubMed]
    [Google Scholar]
  11. Fu L, Niu B, Zhu Z, Wu S, Li W et al. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article][PubMed]
    [Google Scholar]
  12. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
    [Google Scholar]
  13. Rasko DA, Myers GS, Ravel J. Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics 2005; 6:2 [View Article][PubMed]
    [Google Scholar]
  14. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article][PubMed]
    [Google Scholar]
  15. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  16. Moran-Gilad J. Whole genome sequencing (WGS) for food-borne pathogen surveillance and control - taking the pulse. Euro Surveill 2017; 22:30547 [View Article][PubMed]
    [Google Scholar]
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