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.

In Vivo Selection of a Unique Tandem Repeat Mediated Azole Resistance Mechanism (TR120) inAspergillus fumigatus cyp51A, Denmark

“…We subjected total DNA (≈10 ng/µL) to WGS (NextSeq 550; Illumina, https://www.illumina.com) by using Nextera DNA library preparation kit (Illumina) and following the manufacturer’s instructions. We used NASP ( 5 ) to detect single-nucleotide polymorphisms (SNPs) after removal of duplicated regions in the A. fumigatus strain Af293 chromosomes (http://www.aspergillusgenome.org, genome version s03-m05-r09) using NUCmer ( 6 ). We inferred relatedness by using FastTree version 2.1.5 ( 7 ) and a 77.69% core genome (Table; Figure 2).…”

A global to local genomics analysis ofClostridioides difficileST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

“…Simulated reads. Genome assemblies have been shown to provide more noise when inferring the phylogenetic structure of a species compared to raw read data (52). For all publicly available genome assemblies downloaded from GenBank and passing filters, simulated reads were generated with ART (53) version MountRainier with the following command: art_illumina -ss MSv3 -l 250 -f 75 -m 300 -s 30.…”

“…Phylogenetic analyses. To generate a preliminary phylogeny, genome assemblies (n=1,877) were aligned against the finished genome of C. difficile CD630 (GCA_000009205.1) with NUCmer (MUMmer v3.23) (54), and SNPs were called in conjunction with NASP v1.1.2 (52). A maximum likelihood phylogeny was inferred on an alignment of 85,331 concatenated SNPs (Table S2) called from a core genome alignment of 1,860,526 positions with IQ-TREE v1.6.1 (55) using the best-fit model (GTR+F+ASC+R5) identified by ModelFinder (56) SNPs were called from the alignments with the Unified Genotyper method in GATK v3.3-0 (61,62).…”

Neptune: A Bioinformatics Tool for Rapid Discovery of Genomic Variation in Bacterial Populations

“…Some tools have emerged. Most of these tools focus on the identification of single nucleotide variants (SNVs) using reference mapping approaches [6,19], or distance estimations based on small exact substrings (k -mers) [10,15,22] since these approaches scale well using simple parallelization strategies. Microbial genome-wide association studies (GWAS) that analyze bacterial genome populations to correlate genomic features with phenotypic traits are now also possible thanks to recent methodological developments that address the problems inherent in bacterial genomes that confound conventional GWAS approaches, such as long range linkage disequilibrium and clonal population structure [8].…”