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EasyQC: Tool with Interactive User Interface for Efficient Next-Generation Sequencing Data Quality Control.

Vijaya Raghavan Rangamaran1, Bharathram Uppili2, Dharani Gopal1

  • 1Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Chennai, India.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|September 12, 2018
PubMed
Summary

EasyQC is a new graphical tool that simplifies next-generation sequencing (NGS) data quality control. It effectively filters erroneous reads, improving genomic analysis accuracy and efficiency for researchers.

Keywords:
NGSdownstream processinggraphical interfacequality control

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) generates vast amounts of genomic data, crucial for research insights.
  • Sequence errors in NGS data can significantly impact downstream analyses, leading to misleading conclusions.
  • Existing NGS data quality control tools often rely on command-line interfaces, posing usability challenges.

Purpose of the Study:

  • To develop EasyQC, a user-friendly graphical tool for next-generation sequencing data quality control.
  • To provide comprehensive quality control features including read trimming, format conversion, and adapter removal.
  • To enhance the accuracy and efficiency of downstream genomic analyses through improved data quality.

Main Methods:

  • Developed EasyQC with a graphical user interface (GUI) using PERL modules.
  • Implemented features for trimming reads based on quality, length, homopolymer, and ambiguous bases.
  • Integrated tools for format conversion, paired-end merging, adapter trimming, and quality/composition graphing.

Main Results:

  • EasyQC demonstrated a significant increase in overall sequence quality after processing raw NGS data.
  • The tool proved to be relatively fast when tested on standalone desktops with various NGS datasets.
  • EasyQC offers cross-platform compatibility, running on both Windows and Linux systems.

Conclusions:

  • EasyQC provides an accessible and efficient solution for next-generation sequencing data quality control.
  • Its graphical interface and diverse features facilitate easier and more reliable downstream genomic analyses.
  • EasyQC is a valuable addition to the bioinformatics toolkit for researchers working with NGS data.