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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Sequences01:29

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Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...
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CoverView: a sequence quality evaluation tool for next generation sequencing data.

Márton Münz1, Shazia Mahamdallie1,2, Shawn Yost1,2

  • 1Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.

Wellcome Open Research
|June 9, 2018
PubMed
Summary

CoverView is a new tool for quality control in next-generation sequencing (NGS) data. It provides fast, user-friendly evaluation of sequencing reads and flags regions needing review, ensuring reliable genetic testing results.

Keywords:
NGSQSMQuality Sequencing Minimimumbase qualitydepth of coveragegenetic testingmapping qualityquality assurancequality control

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Robust quality assurance and quality control (QA/QC) are critical for reliable next-generation sequencing (NGS) data analysis.
  • Existing tools may lack flexibility or user-friendliness for comprehensive NGS data evaluation.
  • Clinical genetic testing requires stringent quality metrics to ensure diagnostic accuracy.

Purpose of the Study:

  • To introduce CoverView, a novel, efficient, and user-friendly software tool for evaluating NGS data quality.
  • To enable detailed assessment of sequencing reads, including coverage depth and base/mapping quality metrics.
  • To facilitate automated identification and flagging of regions with suboptimal quality in NGS datasets.

Main Methods:

  • CoverView processes mapped sequencing reads against user-defined genomic regions.
  • It generates detailed quality reports, from chromosome-level summaries to per-base profiles.
  • An interactive graphical user interface (GUI) is provided for intuitive result exploration.

Main Results:

  • CoverView successfully processed TruSight Cancer Panel (TSCP) data from a reference sample in 13 seconds.
  • The tool integrates seamlessly into clinical laboratory pipelines, enhancing quality control.
  • It provides transparent, consistent quality metrics and automatically flags regions below specified thresholds.

Conclusions:

  • CoverView offers a fast, flexible, and user-friendly solution for NGS data quality evaluation.
  • Its automated flagging system aids in the systematic review of suboptimal data.
  • CoverView is easily integrable into existing NGS pipelines, improving the reliability of genetic testing.