Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.

scientific article published on 6 October 2017

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.7717/PEERJ.3893
P932PMC publication ID5782805
P698PubMed publication ID29372115

P50authorSteven DavisQ85835451
P2093author name stringHeather A Carleton
Richa Agarwala
Martin Shumway
Ruth E Timme
Lee S Katz
Mustafa Simmons
Hugh Rand
Glenn E Tillman
William A Klimke
Stephanie Defibaugh-Chavez
Eija K Trees
P2860cites workWhen whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomesQ21559496
Synthesis of phylogeny and taxonomy into a comprehensive tree of lifeQ21714372
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of SalmonellaQ24286921
Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and DatabaseQ28078139
The International Nucleotide Sequence Database CollaborationQ28740983
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomesQ34676711
Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United StatesQ36271801
TreeToReads - a pipeline for simulating raw reads from phylogeniesQ36315196
PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United StatesQ37074851
Diverse sources of C. difficile infection identified on whole-genome sequencingQ37405479
Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome SequencingQ37428445
A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne PathogensQ37694453
Automated reconstruction of whole-genome phylogenies from short-sequence readsQ37716144
Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of Listeria monocytogenes associated with an outbreak linked to cheese, United States, 2013.Q38760765
NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats.Q38872283
Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenesQ39275369
Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and InvestigationQ39841774
Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States.Q40917608
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiologyQ42277652
Guidelines for the validation and application of typing methods for use in bacterial epidemiologyQ44729793
CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence dataQ110949957
P275copyright licenseCreative Commons CC0 LicenseQ6938433
P6216copyright statuscopyrighted, dedicated to the public domain by copyright holderQ88088423
P921main subjectphylogenomicsQ3381973
P304page(s)e3893
P577publication date2017-10-06
P1433published inPeerJQ2000010
P1476titleBenchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
P478volume5

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cites work (P2860)
Q92324034All for one and one for all: the true potential of whole-genome sequencing
Q64124588An Overview of PulseNet USA Databases
Q94473447Closed Genome Sequences of 28 Foodborne Pathogens from the CFSAN Verification Set, Determined by a Combination of Long and Short Reads
Q92538246Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept
Q54968691Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.
Q90546825Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform
Q113307732Mashtree: a rapid comparison of whole genome sequence files
Q90116664OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling
Q91198605Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology
Q96302881Ten recommendations for supporting open pathogen genomic analysis in public health
Q64125686The Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains
Q64133058The use of next generation sequencing for improving food safety: Translation into practice
Q64056630Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: as a Proof-of-Concept
Q92511151cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis

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