Whole genome sequence based typing systems
Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole Genome Sequence Based Typing of Listeria monocytogenes
... 300,000 typing entries originating from ⬎ 100 countries, might serve as a blueprint for such service ...of typing schemes to present typing as we see today with the in silico extraction of classical ...
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Epidemiological Typing of Serratia marcescens Isolates by Whole Genome Multilocus Sequence Typing
... marcescens. The calculation engine’s quality-controlled de novo assembly possibilities allow for rapid push-button assembly of WGS data without the need of local computing power. In short, even high-resolution ...
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Pan PCR, a Computational Method for Designing Bacterium Typing Assays Based on Whole Genome Sequence Data
... informative typing methods to monitor bacterial isolates. PCR-based typing assays are fast and inexpensive, but their utility is limited by the lack of targets which are capable of distinguishing ...
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Whole Genome Multilocus Sequence Typing of Extended Spectrum Beta Lactamase Producing Enterobacteriaceae
... Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identifi- cation of sources and routes of transmission in outbreak settings, but current methods ...
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Hash Based Core Genome Multilocus Sequence Typing for Clostridium difficile
... the whole genome. It should be noted that undertaking SNP-based analyses from alignments of de novo assemblies without further filtering of variants would be similarly ...filtering based on ...
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On the SNP-based and Sequence-based Whole Genome Studies for Complex Traits.
... demonstrate its utility. The criteria we used to measure our method’s performance against expert filters are: (i) percentage of SNPs excluded due to low quality; (ii) inflation factor of the test statistics (λ); (iii) ...
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Whole-genome sequence of Schistosoma haematobium
... 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites 8,9 ...included genome annotation based on function, ...
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Whole Genome Sequence of a Turkish Individual
... IKB analysis revealed three interaction networks that included 15, 13, and 3 of the 47 genes. In Figure 3 and Figure S8, we show the first two networks where corresponding drug and hereditary and neurological ...
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SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data
... ABSTRACT Typing of methicillin-resistant Staphylococcus aureus (MRSA) is impor- tant in infection control and ...quence typing (MLST) or equivalent methods like spa typing and typing of the ...
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To Get the Whole Picture, Sequence the Whole Genome Comparing whole genome sequencing and exome sequencing
... DNA sequence for these projects ...probe sequence based on the reference genome can result in probes which hybridize ...to sequence the exome at high accuracy and completeness may be to ...
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Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome Wide Typing of Clostridium difficile
... methods based on whole-genome se- quencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are ...core ...
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Multilocus Sequence Typing of Total Genome Sequenced Bacteria
... multilocus sequence typing (MLST) is considered the “gold standard” of typing, but it is traditionally performed in an expensive and time-consuming man- ...of whole-genome sequencing ...
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Phylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole Genome Sequencing Data
... PGG based on sequence data, as shown in ...SCG based on the sequence data ...yield sequence data for all nine loci, and SCG-3a was not represented in the data ...
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Real Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole Genome Multilocus Sequence Typing
... “core genome” analysis at the level of shared ...the Genome Comparator at all 1,587 shared loci, and gene differences were ...the Genome Comparator analyses is provided in ...
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Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole Genome Sequence Data Using Validation Guidelines
... to sequence data and would have the ability to change on ...of typing panel isolates con- tained a full set of typeable genes using the rMLST scheme or the cgMLST schemes with 50, 100, 500, or 1,455 ...of ...
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Accuracy of imputation to whole-genome sequence in sheep
... Genomic prediction The estimates of genomic heritability (Fig. 10) suggest that using the Minimac3 R 2 statistic to pre-filter WGS variants before selecting subsets for downstream stud- ies such as genomic prediction or ...
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Whole Genome Mapping: a New Paradigm in Strain Typing Technology
... strain typing, comparative genomics, and whole-genome sequence as- sembly and is currently referred to as “whole-genome mapping” ...some. Whole-genome maps, with ...
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Evaluation of Whole Genome Sequencing for Identification and Typing of Vibrio cholerae
... serological typing results were compared with the genome-derived spe- cies identification and serotype for a subset of isolates (n ⫽ ...the whole-genome sequenc- ing (WGS) analysis for the ...
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Core Genome Multilocus Sequence Typing Scheme for High Resolution Typing of Enterococcus faecium
... allele- based approach is that it treats both a genetic mutation, which creates an SNP, and a genetic recombination event, which likely introduces multiple SNPs, correctly as one evolutionary event (24, 29), which ...
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Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum
... core genome SNP typing and cgMLST performed equally in typing our samples and their results were similar, evidencing the validity of cgMLST to be used for ...core genome SNP typing in ...
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