[PDF] Top 20 Empirical assessment of sequencing errors for high throughput pyrosequencing data
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Empirical assessment of sequencing errors for high throughput pyrosequencing data
... the errors of a specific sequenc- ing platform can be approached at many different levels of abstraction since each step of the process is prone to introduce ...automated sequencing- by-synthesis procedure, ... See full document
13
Read Annotation Pipeline for High-Throughput Sequencing Data
... reads leads to underestimation of expression level of genes with variations[18]. Several attempts have been made to create a sample-specific reference genome or transcriptome for alignments. Keane et al. [7] aligned ... See full document
8
Probabilistic methods for quality improvement in high-throughput sequencing data
... kmers. Sequencing errors mutate the valid kmers, populating erroneous kmers into the k-spectrum, which appear as tight “clouds” surrounding true ...neighboring high-frequency ...achieves ... See full document
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Computational approaches for metagenomic analysis of high-throughput sequencing data
... generation sequencing Since 2005, several new methods have displaced Sanger and have become the most common sequencing ...generation sequencing systems” 2012 for more information ... See full document
142
Genotype-Frequency Estimation from High-Throughput Sequencing Data
... improving high-throughput sequencing technologies provide unprecedented opportunities for carrying out population-genomic studies with various ...from sequencing errors and biparental ... See full document
24
Developing High-Throughput HIV Incidence Assay with Pyrosequencing Platform
... a pyrosequencing platform to parallelize genomic HIV incidence assays in pursuit of a single-assay ap- proach scalable for use in routine cross-sectional ...next-generation pyrosequencing as well as those ... See full document
14
Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations
... Next-generation sequencing is an ef fi cient method that allows for substantially more markers than previous technologies, providing opportunities for building high-density genetic linkage maps, which ... See full document
12
Salmonella Serotype Determination Utilizing High Throughput Genome Sequencing Data
... genomes data set was somewhat lower; we were unable to confirm the accuracy of the annotated serotype for those ...serotyping errors and not errors of our ... See full document
8
Comprehensive evaluation of error correction methods for high-throughput sequencing data
... RNA sequencing has significantly revolutionized the study of genomics and molecular ...of high-throughput sequencing technologies have brought about a quick and cheaper way to sequence ...for ... See full document
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Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data
... the sequencing data are assumed to be conditionally inde- pendent between loci given the true genotype ...same sequencing read across ...genotyping errors resulting from low read depth when ... See full document
12
Optimizing a MapReduce Module of Preprocessing High-Throughput DNA Sequencing Data
... handle data communication between the Map() and Reduce() functions of the MapReduce framework in a bioinformatics application that detects and corrects sequencing errors in the NGS ...NGS data ... See full document
6
Universal Count Correction for High-Throughput Sequencing
... mapping data transformation by assuming that the read counts arise from a degenerate count distribution, where the number of bases with non-zero reads is drawn from a binomial, and the number of reads at non-zero ... See full document
11
Improving quality of high-throughput sequencing reads
... HTS data is that there is no standard way to compare error correction tools or to quantitatively analyze their outputs, which is needed to choose a method suitable for the user's ...many errors are ... See full document
109
Detecting non allelic homologous recombination from high throughput sequencing data
... ... vs. Figure 2 Schematic example of our model’s approach to detecting NAHR events from paired-end read data. The bottom half shows our framework for repeats and potential NAHR events. Each pair of homologous ... See full document
19
Recent advances in inferring viral diversity from high-throughput sequencing data
... remove errors introduced in the ligation step of the PCR or during reverse tran- scription ( Seifert et ...the errors stem from RT substitut- ions. The novel circle sequencing (CirSeq) protocol can ... See full document
17
Tools and best practices for retrotransposon analysis using high-throughput sequencing data
... We also studied the specific case of TEtools, which quantifies TEs using randomly reported reads with Bow- tie or Bowtie2. However, this tool considers a list of TE sequences extracted from a genome or manually anno- ... See full document
12
Recent advances in inferring viral diversity from high-throughput sequencing data
... Gerstung et al., 2012; McElroy et al., 2013). Provided reads are mapped onto a reference sequence, an SNV is called as such when a non-reference base is observed more often than expected under a given error model. ... See full document
16
Improved detection of artifactual viral minority variants in high-throughput sequencing data
... Combined, the SSE and HCPP analysis led to a near 95% reduction of identified positions with increased MMF’s in RT- PCR amplified genomes from reverse-genetics generated virus samples, providing a simple and efficient ... See full document
13
Statistical approaches to harness high throughput sequencing data in diverse biological systems
... utilising data stemming from multiple high throughput sequencing technologies to develop novel statistical ...each data type and the context in which it is used has unique ... See full document
180
Empirical Investigations OF RNA Fitness Landscapes: Harnessing the Power of High-Throughput Sequencing and Evolutionary Simulations
... a high level of sequence conservation as compared to the human CPEB3 sequence ...deep sequencing of in vitro co-transcriptional self-cleavage ...these data to reconstruct the phylogenetic fitness ... See full document
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