title: NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats.
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.
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.|2​Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Sahl
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: Darrin
authors.initials: D
authors.lastname: Lemmer
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Travis
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Schupp
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Gillece
authors.affiliation: 3​The George Washington University, 2121 I St NW, Washington, DC 20052, USA.
authors.forename: Maliha
authors.initials: M
authors.lastname: Aziz
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Driebe
authors.affiliation: 4​University of New Hampshire, 105 Main St, Durham, NH 03824, USA.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Drees
authors.affiliation: 5​Harvard University, Cambridge, MA 02138, USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Hicks
authors.affiliation: 2​Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA.
authors.forename: Charles Hall Davis
authors.initials: CHD
authors.lastname: Williamson
authors.affiliation: 2​Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA.
authors.forename: Crystal M
authors.initials: CM
authors.lastname: Hepp
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: David Earl
authors.initials: DE
authors.lastname: Smith
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: Chandler
authors.initials: C
authors.lastname: Roe
authors.affiliation: 1​Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Engelthaler
authors.affiliation: 2​Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Wagner
authors.affiliation: 2​Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
mesh_terms: D003198:Computer Simulation; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D017720:Molecular Epidemiology / Q000379:methods*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software; D000073336:Whole Genome Sequencing / Q000379:methods*
keywords: Phylogeography; SNPs; bioinformatics