The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets

Jw, Sahl; Lemmer, Darrin; Travis, Jason; Jm, Schupp; Jd, Gillece; Aziz, Maliha; Em, Driebe; Drees, Kevin P.; Hicks, Nathan D.; Ch, Williamson; Hepp, Crystal M.; Smith, David Earl; C, Roe; Dm, Engelthaler; Dm, Wagner; Keim, Paul

doi:10.1101/037267

Cited by 22 publications

(18 citation statements)

References 43 publications

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“…Overall, we identified and confirmed a total of 716 nucleotide substitutions relative to the VARV reference sequence by eye and using NASP [16] in conjunction with GATK [17], with a minimum of 5× coverage and 0.9 frequency. We also enriched for, sequenced, and produced a mitochondrial genome at 193× coverage.…”

Section: Resultsmentioning

confidence: 99%

17th Century Variola Virus Reveals the Recent History of Smallpox

et al. 2016

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SummarySmallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1, 2, 3, 4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4, 5, 6, 7, 8, 9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4, 5, 6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.

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Section: Resultsmentioning

confidence: 99%

17th Century Variola Virus Reveals the Recent History of Smallpox

et al. 2016

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“…Furthermore, the threshold used is only valid for the workflow used to generate SNP pairwise distances. Other variant calling workflow would result in different distributions (Sahl et al, 2016), and thus different thresholds.…”

Section: Resultsmentioning

confidence: 99%

Closing gaps for performing a risk assessment on Listeria monocytogenes in ready‐to‐eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis

Nielsen

Björkman

Kiil

et al. 2017

EFSA Supporting Publications

111

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This report presents the results of the project "Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis". The main objective was to compare L. monocytogenes isolates collected in the EU from ready-to-eat (RTE) foods, compartments along the food chain and from human cases by the use of WGS. A total of 1,143 L. monocytogenes isolates were selected for the study, including 333 human clinical isolates and 810 isolates from the food chain. The isolates were whole genome sequenced. The phylogeny showed a clear delineation between L. monocytogenes lineages and between clonal complexes within lineages. A range of typing methods were applied to the sequence data, providing the framework to answer questions on genetic diversity and epidemiological relationships. Retrospective analysis of nine outbreaks showed that WGS is a powerful tool in national and international outbreak investigations as WGS can accurately rule isolates in or out of outbreaks. Source attribution models showed bovine reservoir to be the main source of human disease although other sources also contributed and generally confidence intervals were high. Numerous consistent genetic linkages between a priori unlinked strains were identified, some of which involved isolates from multiple countries. The presence of putative markers conferring the potential to survive/multiply in the food chain and/or cause disease in humans was explored by detecting the presence of putative virulence genes, AMR genes and factors conferring the ability to persist in the food processing chain. This study has demonstrated one of the major benefits of WGS, which is the ability to address a wide range of questions including those on virulence, antimicrobial resistance, source attribution, surveillance and outbreak detection and investigation, in a single experiment.

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“… A core genome single-nucleotide-polymorphism (SNP) phylogeny of Burkholderia genomes. All SNPs were identified by aligning genome assemblies against the finished genome of B. pseudomallei K96243 ( 19 ) with NUCmer ( 20 ) and processed with the Northern Arizona SNP Pipeline ( http://tgennorth.github.io/NASPtgennorth.github.io/NASP ) ( 30 ). A maximum-likelihood phylogeny was inferred on the concatenated SNP alignment with RAxML version 8 ( 31 ) with 100 bootstrap replicates.…”

Section: Resultsmentioning

confidence: 99%

The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

Sahl

Vazquez

Hall

et al. 2016

mBio

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Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.

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The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets

Cited by 22 publications

References 43 publications

17th Century Variola Virus Reveals the Recent History of Smallpox

17th Century Variola Virus Reveals the Recent History of Smallpox

Closing gaps for performing a risk assessment on Listeria monocytogenes in ready‐to‐eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis

The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

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