ArticleMicrobial genomics2016
NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats.
Article in Microbial genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 202 papers.
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202 citing papers in PubMed.
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- From colonizer to culprit: genomic and clinical insights into S. epidermidis from post-surgical endophthalmitis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
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- Reliability of disc diffusion testing and molecular epidemiology of penicillin-susceptible Staphylococcus aureus bacteraemia.The Journal of antimicrobial chemotherapy · 2025Article
142 more citing papers are in PubMed but not listed here.
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16 authors.
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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.
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