NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats

Jason W. Sahl, Darrin Lemmer, Jason Travis, James M. Schupp, John D. Gillece, Maliha Aziz, Elizabeth M. Driebe, Kevin P. Drees, Nathan D. Hicks, Charles Hall Davis Williamson, Crystal M. Hepp, David Earl Smith, Chandler Roe, David M. Engelthaler, David M. Wagner, Paul Keim

Research output: Contribution to journalArticle

63 Scopus citations

Abstract

Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces similar, and often better, results in comparison with other pipelines, but is much more flexible in terms of data input types, job management systems, diversity of supported tools and output formats. We also demonstrate differences in results based on the choice of the reference genome and choice of inferring phylogenies from concatenated SNPs or alignments including monomorphic positions. NASP represents a source-available, version-controlled, unit-tested method and can be obtained from tgennorth.github.io/NASP.

Original languageEnglish (US)
Pages (from-to)e000074
JournalMicrobial Genomics
Volume2
Issue number8
DOIs
StatePublished - Aug 1 2016

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Keywords

  • Phylogeography
  • SNPs
  • bioinformatics

ASJC Scopus subject areas

  • Epidemiology
  • Microbiology
  • Molecular Biology
  • Genetics

Cite this

Sahl, J. W., Lemmer, D., Travis, J., Schupp, J. M., Gillece, J. D., Aziz, M., Driebe, E. M., Drees, K. P., Hicks, N. D., Williamson, C. H. D., Hepp, C. M., Smith, D. E., Roe, C., Engelthaler, D. M., Wagner, D. M., & Keim, P. (2016). NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microbial Genomics, 2(8), e000074. https://doi.org/10.1099/mgen.0.000074