Synflow is a powerful web application for visualizing genome alignments and structural variations using SyRI (Structural Rearrangement Identifier) data. It provides an interactive platform for exploring genomic synteny, inversions, translocations, duplications, and other structural rearrangements between genomes.
Synflow is available for free to use at synflow.southgreen.fr
A more descriptive documention of SynFlow is available https://synflow.readthedocs.io/en/latest/
A Snakemake workflow to detect synteny blocks and identify chromosomal rearrangements https://gitlab.cirad.fr/agap/cluster/snakemake/synflow
- Use precomputed datasets or run your own analysis
- Chain multiple genome comparisons for comprehensive analysis
- Drag and drop chromosomes to reorder them
- Detailed control panel for customizing visualizations
- Download the visualization as an SVG file
- Files must be in SyRI output format. See the SyRI documentation
- The file names should follow the pattern: ref-genome_query-genome.out
- Files can be chained for multiple genome comparisons:
Example of file chain:
- A-thaliana_C-rubella.out
- C-rubella_B-rapa.out
- B-rapa_O-sativa.out
This will create a visualization chain: A-thaliana → C-rubella → B-rapa → O-sativa
- Existing files: select from precomputed datasets. The available files come from analyses performed on several organisms using the workflow See the documentation
- Run analysis: run workflow using fasta + gff3 files (optional)
- Browse FTP: import files directly from an FTP server by providing the URL
- Upload file: use the "Browse" button to upload your own files
Use the zoom and pan features to explore the visualization.
Chromosome order can be changed by drag and drop.
SynFlow's rendering performance scales with the complexity of the genomic data and the user's hardware capabilities. Key factors affecting performance include:
- Data size: Rendering time increases with the number of synteny bands, chromosomes, and genomes.
- Genome chaining: Up to 20 genomes can be chained for comprehensive comparisons, but this may impact performance for very large datasets.
- Hardware requirements: Optimal performance requires at least 4 CPU cores and 8 GB RAM. More cores and memory significantly reduce rendering times.
Limitations:
- Input data must be in SyRI output format (.out files) with specific naming conventions.
- Maximum supported file sizes depend on browser and server limits (typically up to 100MB for uploads).
- Requires a modern web browser with support for SVG rendering (Chrome 80+, Firefox 75+, Safari 13+).
- Analysis workflows are limited to the available computational resources on the server.
SynFlow provides a performance metrics dashboard accessible at https://synflow.southgreen.fr/metrics.html. This interactive tool visualizes rendering performance data collected from user analyses, displaying charts that correlate rendering duration with various parameters such as:
- Number of synteny bands
- Number of chromosomes
- Number of genomes in the chain
- CPU core count
- Available memory
The dashboard helps users understand performance expectations, optimize their data preparation, and make informed decisions about hardware requirements for large-scale genomic analyses.
This project is licensed under the terms of the GNU General Public License v3.0. See the LICENSE file for details.
- Marilyne Summo
- Gaëtan Droc
- Mathieu Rouard
- Gautier Sarah
See also the list of contributors who participated in this project.