End-to-End Pipeline Automation
Generate, execute, visualize, and share reproducible Snakemake pipelines with AI.
Get Started
Why Autopipe?
AI Pipeline Generation
Describe your analysis in natural language. Claude AI generates a complete Snakemake pipeline with Dockerfile, config, and metadata.
Docker Execution
Run pipelines in Docker containers on remote SSH servers. Fully reproducible environments with automated build and execution.
Registry Integration
Search AutoPipeHub and WorkflowHub simultaneously. Import existing workflows and extend them with your own analysis steps.
Interactive Viewer
Browse results directly in the browser. Built-in support for IGV genomics, images, tables, PDFs, and HDF5 with extensible plugins.
Viewer Plugins
Extend the built-in result viewer with plugins for specialized file formats.
IGV Genomics
Visualize BAM, VCF, BED, and GFF files with IGV.js. Supports reference genome selection for interactive genome browsing.
Image Viewer
Display PNG, JPG, SVG, and TIFF scientific images. Zoom, pan, and compare experimental result images side by side.
Data Table
Render CSV and TSV files as sortable, filterable tables. Quickly inspect pipeline output metrics and summary statistics.
PDF & HDF5
View PDF documents and browse HDF5 scientific data files. Navigate hierarchical datasets directly in the result viewer.
Get Autopipe Desktop
Download the desktop app to create, execute, and manage bioinformatics pipelines with Claude AI.