Releases: SouthGreenPlatform/SynFlow
V1.0.0 - Initial Release
SynFlow V1.0.0 Release Notes
Welcome to SynFlow V1!
We are thrilled to announce the first major release of SynFlow, a powerful web application for visualizing genome alignments and structural variations. SynFlow enables researchers to interactively explore genomic synteny, inversions, translocations, duplications, and other structural rearrangements between multiple genomes.
Key Features
Core Visualization
- Interactive Genome Alignment Visualization: Explore complex structural variations between multiple genomes with intuitive zoom and pan controls
- SyRI Data Support: Full compatibility with SyRI (Structural Rearrangement Identifier) output files for comprehensive genomic analysis
- Multi-Genome Chains: Chain multiple SyRI output files to visualize comparative genomics across multiple species
Data Input Flexibility
- Multiple Input Options:
- Explore precomputed datasets from the built-in database
- Upload your own SyRI output files (.out)
- Import files directly from FTP servers
- Run custom workflows for data analysis
Advanced Controls
- Intelligent Filtering: Filter genomic bands by type and length using interactive legends and sliders
- Export Capabilities: Download visualizations as SVG files for publications and presentations
- Flexible Chromosome Ordering: Drag-and-drop functionality to reorganize chromosomes for better visualization
Web Application
- Free Online Platform: Access SynFlow at synflow.southgreen.fr
- Docker Support: Easy deployment with Docker and Docker Compose
Documentation
Comprehensive documentation is available at synflow.readthedocs.io, including:
- Detailed feature guides
- Input data format specifications
- Analysis workflow instructions
- Visualization control panel documentation
Data Analysis Workflow
For generating and preparing your data for SynFlow visualization, please refer to our Snakemake workflow:
Contributing
We welcome contributions from the community! Please visit our GitHub repository to:
- Report bugs or request features
- Submit pull requests
- Participate in discussions
License
SynFlow is licensed under the GNU General Public License v3.0. See the LICENSE file for details.
Acknowledgements
Authors:
- Marilyne Summo
- Gaëtan Droc
- Mathieu Rouard
- Gautier Sarah
Special Thanks:
- The SyRI development team for their outstanding structural rearrangement identification tool
- The PlotSR project for inspiration
- All contributors and users who have provided feedback and support
Support
For questions, feature requests, or bug reports, please:
- Check the documentation
- Visit our GitHub Issues
- Contact the development team
Thank you for using SynFlow! We hope it enhances your genomic research.