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CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and

Jeffrey W Grover1, Matthew Bomhoff2,3, Sean Davey2,3

  • 1Department of Molecular and Cellular Biology University of Arizona Tucson AZ USA.

Plant Direct
|June 27, 2019
PubMed
Summary
This summary is machine-generated.

LoadExp+ enhances biological research by providing accessible genomic and epigenomic analyses. This bioinformatics suite integrates with CoGe, enabling diverse analyses for researchers of all skill levels.

Keywords:
ChIP‐seqDNA methylationRNA‐seqSNP identificationbisulfite sequencingepigenomicsexpression analysisgenomicsnext‐generation sequencingpopulation genetics

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Area of Science:

  • Bioinformatics
  • Genomics
  • Epigenomics

Background:

  • Genomic and epigenomic analyses are crucial for biological research.
  • Wider accessibility to these analyses is needed for the research community.

Purpose of the Study:

  • To create a user-friendly platform for genomic and epigenomic data analysis.
  • To integrate various bioinformatics workflows into a single system.

Main Methods:

  • Development of LoadExp+, a suite of bioinformatics workflows.
  • Integration of LoadExp+ with the CoGe comparative genomics platform.
  • Enabling transcriptomic (RNA-seq), epigenomic (bisulfite-seq), and ChIP-seq analyses.

Main Results:

  • LoadExp+ supports transcriptomic, epigenomic, chromatin-binding, variant identification, and population genetics analyses.
  • All analyses are integrated with CoGe for visualization and downstream processing.
  • Data can be exported to CyVerse for further management and analysis.

Conclusions:

  • LoadExp+ increases accessibility of complex genomic and epigenomic analyses.
  • The platform facilitates data management throughout the entire lifecycle.
  • It empowers researchers of all skill levels to perform advanced bioinformatics analyses.