(Q38872283)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

title

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

1 reference

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14 March 2020

1 reference

2

1 reference

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14 March 2020

14

David M Engelthaler

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

11

Crystal M Hepp

1 reference

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14 March 2020

16

Paul Keim

1 reference

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14 March 2020

author name string

Jason W Sahl

1

1 reference

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14 March 2020

Jason Travis

3

1 reference

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14 March 2020

James M Schupp

4

1 reference

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14 March 2020

John D Gillece

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Maliha Aziz

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Elizabeth M Driebe

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Kevin P Drees

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Nathan D Hicks

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Charles Hall Davis Williamson

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

David Earl Smith

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Chandler Roe

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

David M Wagner

15

1 reference

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14 March 2020

publication date

25 August 2016

1 reference

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14 March 2020

1 reference

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14 March 2020

volume

2

1 reference

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14 March 2020

issue

8

1 reference

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14 March 2020

page(s)

e000074

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

Hypervirulent emm59 Clone in Invasive Group A Streptococcus Outbreak, Southwestern United States

14 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Defining the phylogenomics of Shigella species: a pathway to diagnostics

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Trimmomatic: a flexible trimmer for Illumina sequence data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Automated reconstruction of whole-genome phylogenies from short-sequence reads

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Using PLINK for Genome-Wide Association Studies (GWAS) and data analysis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Fast gapped-read alignment with Bowtie 2

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

ART: a next-generation sequencing read simulator.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Genomic anatomy of Escherichia coli O157:H7 outbreaks

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

A framework for variation discovery and genotyping using next-generation DNA sequencing data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Mugsy: fast multiple alignment of closely related whole genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

FastTree 2--approximately maximum-likelihood trees for large alignments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

The Sequence Alignment/Map format and SAMtools

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Whole-genome-based phylogeny and divergence of the genus Brucella

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Genome sequence of Yersinia pestis, the causative agent of plague

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

The complete genome sequence of Escherichia coli K-12

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Recombination in Escherichia coli and the definition of biological species

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

ExaBayes: massively parallel bayesian tree inference for the whole-genome era.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

Using MUMmer to identify similar regions in large sequence sets.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5320593

22 August 2018

Identifiers

DOI

10.1099/MGEN.0.000074

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28348869%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

PubMed publication ID

28348869

1 reference