figeno

Figeno generates publication-quality figures for genomics, focusing on multi-region views across genomic breakpoints, long reads with base modifications, and epigenomic data.

Key Features:

• Multi-region visualization: Generates figures showing multiple genomic regions simultaneously, including across genomic breakpoints.
• Long-read support: Visualizes long reads with base modifications.
• Epigenomic data support: Supports ATAC-seq, ChIP-seq, and HiC data types.
• Whole genome sequencing support: Visualizes copy numbers and structural variants from whole genome sequencing data.

Scientific Applications:

• Genomic breakpoint analysis: Creates multi-region views to visualize genomic rearrangements and breakpoints.
• Epigenomic data integration: Generates figures combining chromatin accessibility, histone modifications, and chromosome conformation data.
• Structural variant visualization: Produces figures displaying copy number alterations and structural variants from whole genome sequencing.
• Modified base detection in long reads: Visualizes base modifications detected in long-read sequencing data.

Methodology:

Figeno is implemented as a Python package with both command-line and graphical user interfaces.