Squiggy - Positron Extension¶
Squiggy is a Positron IDE extension for visualizing Oxford Nanopore sequencing data from POD5 files directly in your workspace.
Documentation¶
- User Guide - Complete guide to using the extension
- Multi-Sample Comparison Guide - Compare 2+ POD5 datasets with delta tracks
- Quick Reference - Commands, shortcuts, and common workflows
- Developer Guide - Setup and contribution guide
- API Reference - Python package documentation
Features¶
- Positron Integration: Works with your active Python kernel
- Interactive Visualization: Bokeh-powered plots with zoom, pan, and hover
- Base Annotations: Overlay base calls on signal data (requires BAM file)
- Read Filtering: Search by read ID, reference region, or sequence motif
- Modification Analysis: Filter and visualize base modifications with probability thresholds
- Multi-Sample Comparison: Load 2-6+ samples and compare with delta tracks showing differences
System Requirements¶
- Positron IDE: Version 2024.09.0 or later
- Operating Systems: macOS (Intel/Apple Silicon), Linux, Windows
- Python: 3.12 or later
- Memory: 4GB RAM minimum (8GB recommended for large POD5 files)
- Disk Space: Varies by dataset size (POD5 files can be several GB)
Installation¶
Install from OpenVSX (Recommended)¶
- Open Positron IDE
- Open Extensions panel (
Cmd+Shift+X/Ctrl+Shift+X) - Search for "Squiggy"
- Click Install
Or visit the OpenVSX marketplace page.
First Time Setup¶
After installing the extension, a Setup panel will appear in the sidebar if the Python package is not detected. The panel provides:
- Step-by-step instructions to create a virtual environment
- Copy-paste commands for installation
- Direct link to select your Python interpreter
- Automatic verification of setup completion
No command-line experience needed—just follow the guided setup!
Alternative: Install from VSIX¶
Download the latest .vsix file from GitHub Releases and install via Extensions → ... → Install from VSIX...