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Whole-genome re-sequencing data

INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance

INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance

... drug re- sistance mutations, (iii) perform early season risk assess- ment, (iv) strengthen vaccine effectiveness analysis, and (v) optimize pre-season vaccine strain ...phylogenetic data (downstream ...NGS ...

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Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

... Six markers were dominant in these 21 isolates, and the other 76 markers were co-dominant. The relatively high PIC and relatively low observed heterozygosity could be due to a higher conservation of these SSR loci among ...

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Enhanced de novo assembly of high throughput pyrosequencing data using whole genome mapping.

Enhanced de novo assembly of high throughput pyrosequencing data using whole genome mapping.

... continuous genome coverage across the resulting merged ...draft genome sequence was aligned with the WGRM to identify discordant ...by re-alignment to the WGRM, after merging them ...full ...

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Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.

Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.

... variant data from whole genome, exome, and targeted re- ...to whole genome sequence data in apparently unrelated individuals yields a parsimonious set of variants for ...

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Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

... sequence data generation The blood samples of all 38 Singapore Indians were extracted from the Singapore BioBank, and DNA extraction was performed at the Defence Medical and Enviromental Research Institute ...

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Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades

Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades

... draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary ...gigas genome was assembled with 103 Gb raw reads sequenced in an Illumina ...draft ...

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Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

... To address this question, we evaluated WGS-based genotyping for tracking the continuous spread of Mtb in a metropolitan setting, and for precisely calibrating the short-term evolution of the genome of Mtb by ...

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Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.

Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.

... genotype data is important for plant and animal breeding, medicine, and evolutionary ...by sequencing the Drosophila Genetic Reference Panel population of inbred ...SNP data and used it in a genomic ...

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Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015

Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015

... to re- sequence is too long compared with the time frame within which action should be ...reference genome with at least 70% nt identity were kept and used to determine the proportion of the query ...

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The impact of post-alignment processing procedures on whole-exome sequencing data

The impact of post-alignment processing procedures on whole-exome sequencing data

... much richer picture of human variation across regions and/ or populations (Haga, 2017; Wijmenga and Zhernakova, 2018; Stark et al., 2019). In Latin America, one of the first initiatives was the Brazilian Initiative on ...

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PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

... the genome, and which do not change over ...WGS data for an isolate into a series of identifiers, one per ...WGS data have differing poli- cies on data sharing, so a global allele nomenclature ...

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The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

... and re- quire culture and manipulation of large numbers of highly infectious ...lar genome and so molecular determination of resistance offers a rapid, potentially cost effective, and safer alter- ...

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McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data

McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data

... WGS data provide some measure of their own performance relative to using simulations, benchmark genomic data, or PCR-based ...genomic data, which revealed many method-specific predictions and ...

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A gene based bacterial whole genome comparison toolkit.

A gene based bacterial whole genome comparison toolkit.

... through whole-genome align- ment [ 34 ...pairwise genome comparison for bac- teria and eukaryotes [ 35 , 36 ], where the application and the visualization shown good ...the whole population of ...

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Whole genome and exome sequencing of monozygotic twins with trisomy 21, discordant for a congenital heart defect and epilepsy.

Whole genome and exome sequencing of monozygotic twins with trisomy 21, discordant for a congenital heart defect and epilepsy.

... VarScan version 2.2.5 was used to identify SNVs from the mpileup alignment data. It compared the read counts, base quality and allele frequency between the twins. Discordant SNVs were called with the ...

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Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

... semi-wild genome Maliaodou and the reference genome Williams ...reference genome; green and purple vertical lines present the intra-chromosomal translocations and inversion events, ...

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Genome sequencing reveals a phage in Helicobacter pylori

Genome sequencing reveals a phage in Helicobacter pylori

... Very little is known about H. pylori phages; however, shortly after the discovery of H. pylori, Marshall et al. (18) and Goodwin et al. (19) described intracellular phage-like particles observed in human gastric mucosa. ...

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Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI 1998-2010.

Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI 1998-2010.

... when sequencing these ...accidentally re-introduced into the population through exposure of laboratory workers, which could also explain the relatively few ...

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Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum.

Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum.

... the genome and is characterized by the chromosome (Chr), position (Pos), and the reference base ...the genome and indicates whether the position is uniquely mappable (if self-mapping coverage = ...

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Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.

Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.

... for sequencing errors and false variant calls, compared with de novo assembly; however, mapping against a reference genome introduces a bias towards the reference sequence that can result in false homology ...

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