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 2025.6.0 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)¶

1. Open Positron IDE
2. Open Extensions panel (Cmd+Shift+X / Ctrl+Shift+X)
3. Search for "Squiggy"
4. Click Install

Or visit the OpenVSX marketplace page.

First Time Setup¶

When you first use Squiggy, it automatically:

1. Creates a dedicated virtual environment at ~/.venvs/squiggy
2. Installs the bundled squiggy Python package using uv
3. Configures a background kernel for extension operations

No manual Python package installation required! The extension handles everything.

Note: The automatic setup requires uv to be installed. If uv is not found, you'll be prompted to install it.

Alternative: Install from VSIX¶

Download the latest .vsix file from GitHub Releases and install via Extensions → ... → Install from VSIX...