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Related Experiment Video

Updated: Jun 24, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Figeno: multi-region genomic figures with long-read support.

Etienne Sollier1,2, Jessica Heilmann1, Clarissa Gerhauser1

  • 1Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

Bioinformatics (Oxford, England)
|June 10, 2024
PubMed
Summary

Figeno is a new tool that generates high-quality genomic figures for publication. It visualizes complex genomic data, including base modifications and structural variants, aiding researchers in data analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Publicly available genomic data is rapidly increasing.
  • Effective analysis and visualization tools are essential for interpreting this data.
  • Current tools may not adequately address specific needs like multi-region genomic views or base modification visualization.

Purpose of the Study:

  • To introduce figeno, a novel application for creating publication-quality figures for genomics.
  • To provide specialized visualization capabilities for genomic breakpoints, long reads with base modifications, and epigenomic data.
  • To offer a user-friendly tool for researchers working with diverse genomic datasets.

Main Methods:

  • Figeno is developed as a Python package.
  • It offers both a command-line interface (CLI) and a graphical user interface (GUI).
  • The application supports various genomic data types, including epigenomic (ATAC-seq, ChIP-seq, HiC) and whole-genome sequencing data (copy numbers, structural variants).

Main Results:

  • Figeno enables the generation of publication-quality figures from complex genomic data.
  • It provides specialized multi-region views across genomic breakpoints.
  • The tool visualizes long reads with base modifications and integrates epigenomic and whole-genome sequencing data.

Conclusions:

  • Figeno addresses the need for advanced visualization tools in genomics.
  • It facilitates the clear presentation of complex genomic features, including base modifications and structural variations.
  • The application enhances the interpretability of diverse genomic and epigenomic datasets for research publications.