sashimi.py

sashimi.py generates programmable visualizations of genomic datasets to display gene annotation, functional domains, isoform expression, chromatin accessibility, and sequencing-derived structures such as those from scRNA-seq and long-read sequencing.

Key Features:

• Versatile visualization of genomic features: Supports visualization of gene annotation with functional domain mapping, isoform expression, and transcript structures identified through scRNA-seq and long-read sequencing.
• Programmable visualization: Provides programmable generation of plots extending traditional sashimi plots for customized analytical outputs.
• Direct raw-data integration: Enables visualization of chromatin accessibility and chromatin architecture directly from raw data inputs.
• Flexible output formats: Produces a broad range of output file formats suitable for downstream analysis and publication.

Scientific Applications:

• Gene annotation and domain mapping: Visualizes functional domains within genes to aid interpretation of gene structure and annotated features.
• Isoform and alternative splicing analysis: Displays isoform expression and exon–junction usage to support studies of alternative splicing.
• Single-cell and long-read sequencing interpretation: Represents cellular heterogeneity and complex transcript architectures derived from scRNA-seq and long-read sequencing data.

Methodology:

Generates sashimi-style and related programmable visualizations directly from genomic and sequencing raw inputs, including representations of chromatin accessibility and transcript structures.