NGS data analysis
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Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer. Accurate variant calling in NGS data is a critical step upon which virtually all downstream analysis and interpretation processes rely.
13p vibransone 28-03-2024 4 2 Download
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In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.
12p vinarcissa 21-03-2023 6 1 Download
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Small bowel adenocarcinomas (SBAs) are rare and there is little comprehensive data on SBA genomic alterations for Asian patients. This study aimed to profile genomic alterations of SBA in Japanese patients using targeted next-generation sequencing (NGS).
10p vikolindagrabar 27-07-2022 4 1 Download
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Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions.
15p vigalileogalilei 27-02-2022 14 2 Download
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Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method of analysing single-read methylome data. Using this method, we identify patterns relating to the mechanism of two plant non-CG-methylating enzymes, CMT2 and DRM2.
19p viarchimedes 26-01-2022 40 0 Download
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Thes tructures of the crystalline compounds were characterized via their spectral analyses. General information about the structures of the newly obtained Hofmann-type clathrates was obtained from their vibration spectra by considering significant changes in the vibration peaks of the cyanide group, water ligand molecule, and guest molecules (water and 1,4-dioxane). The thermal behavior of the Hofmann-type clathrates was investigated in the range of 25–500°C.
14p tudichquannguyet 29-11-2021 7 0 Download
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Next-Generation Sequencing (NGS) has been widely accepted as an essential tool in molecular biology. Reduced costs and automated analysis pipelines make the use of NGS data feasible even for small labs, yet the methods for interpreting the data are not sophisticated enough to account for the amount of information.
12p vigiselle2711 30-08-2021 11 1 Download
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The last 10 years have seen the rise of countless functional genomics studies based on NextGeneration Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two first steps of data analysis consist of a quality control of the raw reads followed by a mapping of those reads to a reference genome/transcriptome.
11p visilicon2711 20-08-2021 6 1 Download
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The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery.
16p vijeeni2711 24-07-2021 13 1 Download
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Mục tiêu nghiên cứu của đề tài là nghiên cứu cơ sở lý luận về hiệu quả hoạt động Ngân hàng, nghiên cứu phương pháp phân tích bao dữ liệu (Data Envelopment Analysis – DEA) và chỉ số đo lường thay đổi năng suất nhân tố tổng hợp Malmquist.
137p thiennhaikhach04 18-07-2021 36 6 Download
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Studies that generate multiple high-throughput NGS datasets require data integration methods for two general tasks: 1) generation of genome-wide data tracks representing an aggregate of multiple replicates of the same experiment; and 2) combination of tracks from different experimenta
7p vijeeni2711 30-06-2021 11 0 Download
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A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima’s D. These statistics are now often being applied in the analysis of Next Generation Sequencing (NGS) data. However, estimates of frequency spectra from NGS data are strongly affected by low sequencing coverage; the inherent technology dependent variation in sequencing depth causes systematic differences in the value of the statistic among genomic regions.
14p viwyoming2711 16-12-2020 11 1 Download
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Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice.
11p vikentucky2711 26-11-2020 11 1 Download
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Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it.
18p vikentucky2711 26-11-2020 10 0 Download
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Next-generation sequencing (NGS) has advanced the application of high-throughput sequencing technologies in genetic and genomic variation analysis. Due to the large dynamic range of expression levels, RNA-seq is more prone to detect transcripts with low expression.
11p vikentucky2711 26-11-2020 13 0 Download
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High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scientists for an efficient, cost and time effective solution to analyse such data. Further, for the different types of NGS data, there are certain common challenging steps involved in analysing those data.
13p vikentucky2711 26-11-2020 21 0 Download
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Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research.
8p vikentucky2711 26-11-2020 10 0 Download
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Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, adaptors and artifacts subject to sequencing errors makes this step non-trivial.
8p vikentucky2711 26-11-2020 8 0 Download
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Quality control is a necessary step of any Next Generation Sequencing analysis. Although customary, this step still requires manual interventions to empirically choose tuning parameters according to various quality statistics.
8p vikentucky2711 24-11-2020 13 2 Download
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Technical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysis and interpretation of RNA sequencing data.
11p vioklahoma2711 19-11-2020 16 1 Download