[PDF] Top 20 Analysis of error profiles in deep next generation sequencing data
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Analysis of error profiles in deep next generation sequencing data
... investigate error profiles and the limits of variant de- tection, we established a truth dataset composed of 19 somatic single-nucleotide variants (SNVs) from the matched cancer/normal cell lines COLO829 ... See full document
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Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage
... In summary, we sought to build an analysis platform suitable to address the problem of estimation of the pop- ulational genetic diversity of RNA viruses. Due to high mutational rates and accelerated replicative ... See full document
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Unraveling genomic variation from next generation sequencing data
... As next generation sequencing (NGS) techniques have become cheaper and more advanced in throughput over time, great innovations and breakthrough conclusions have been generated in various biological ... See full document
25
Estimating Individual Admixture Proportions from Next Generation Sequencing Data
... With next generation sequencing technologies it is possible to obtain genetic data for all accessible genetic variations in the ...admixture analysis rely on known ...low-depth ... See full document
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A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis
... in error correction is that inconsistent genome sampling and genomic repeats may occur at high frequencies and consequently result in numerous equally susceptible cor- rection ...acceptable error threshold ... See full document
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Systematic analysis of transcriptomic profiles of COPD airway epithelium using next-generation sequencing and bioinformatics
... Pathway Analysis (IPA) software (Ingenuity Systems, Redwood City, CA, USA) contains a large data- base with detailed and structured findings reviewed by ...enables analysis, integration, and ... See full document
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Transcriptome Analysis of Reaction Wood in Gymnosperms by Next Generation Sequencing
... Thirty genes were selected from 2875 differentially expressed genes (FDR < 0.05), and qPCR was performed to validate the RNA-Seq results and to identify the genes involved in compression wood formation. In order to ... See full document
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Implementation of Cloud based Next Generation Sequencing data analysis in a clinical laboratory
... Much of the cost so far has been due to human and other errors that have led to re-analysis of several sam- ples. The most common cause so far has been discrep- ancies in the gene names produced from the ordering ... See full document
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Visual programming for next-generation sequencing data analytics
... or data structures cannot be used ...internal data structures like the Burrows-Wheeler transform, used by other pro- grams, like ...sequence analysis and NGS data ...sequence analysis ... See full document
17
Overcoming bias and systematic errors in next generation sequencing data
... Background: clinical applications of microarrays While microarrays were rapidly accepted in research applications, incorporating them in clinical settings has required over a decade of benchmarking, standardization and ... See full document
5
Next generation sequencing in thyroid cancer
... In addition to well-known BRAF, RAS, and RET muta- tions, NGS technology facilitated detection of new somatic alterations in thyroid cancer such as MITF, MDM2, JAK3, FLI1, IDH1 etc. [20], all in which the sig- nificance ... See full document
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Original Article Potential serum microRNA signatures of pediatric IgA nephropathy
... sequence analysis of the plasma microRNAs of pediatric patients with IgA nephropathy and healthy control by next generation sequencing (NGS) using the Illumina Deep Sequencing ... See full document
17
Error Correction in Next Generation DNA Sequencing Data
... an error correction program that targets the Illumina genome sequencer, which is currently the dominant NGS ...advanced data structures with an intricate analysis of data to achieve high ... See full document
44
Original Article The transcriptome difference between vulnerable and stable carotid atherosclerotic plaque
... with next-generation of RNA-seq, then data were ...sequence analysis of the vulnerable and stable carotid atherosclerotic plaque by next generation sequencing (NGS) using ... See full document
17
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data
... DNA sequencing technologies have dramatically increased speed and reduced sequencing ...these sequencing technologies is often challenged by errors and biases associated with the bioinformatical ... See full document
37
CoverView: a sequence quality evaluation tool for next generation sequencing data.
... The Analysis View shows metadata of the analysis such as the names of input files and key configuration ...The Profiles View provides an interactive table and graph of per-base quality ... See full document
12
pTuneos: prioritizing tumor neoantigens from next-generation sequencing data
... the generation of gene muta- tion and leads to production of more potential neoanti- gens, while cytolytic activity, which reflects the activity of immune infiltrate T cells, did not exhibit this ...our ... See full document
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VariantDB: a flexible annotation and filtering portal for next generation sequencing data
... Next generation sequencing (NGS) has the power to screen a whole genome for all kinds of genetic variation in a single experiment ...exome sequencing (WES) typically yields over 20,000 protein ... See full document
10
HLAreporter: a tool for HLA typing from next generation sequencing data
... accuracy, data with good coverage on HLA genes are also ...If sequencing reads were poorly captured during the enrichment process on exonic fragments, it would be unlikely to properly detect HLA ... See full document
12
Adaptive bandwidth kernel density estimation for next generation sequencing data
... To quantitatively demonstrate the qualitative effects described above, we identified all strict local maxima for chromosome 1 in the fixed bandwith h = 362 and the adaptive bandwidth k = 7 curves. The curve f has a ... See full document
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