GraphSNP: What is it?
GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes.When to use
You can use GraphSNP for:- Rapid SNP distance or (other type of distances) network visualisation: No instalation required, drag and drop input files, interactive and easy to use.
- Visualise and investigate distance distribution interactively.
- Create network of pairwise SNP distances and apply SNPs cutoff for cluster analysis.
- Detect and report cluster's membership based on community detection algorithms.
- Create transmission tree based on SNPs and collection day.
How to use
Drag and drop a multi-fasta SNPs alignment or a distance matrix and a metadata file into Input page. Then visualise it at Distances and GraphSNP page.User Manual
For more detailed information about GrapSNP, please download GraphSNP user manual below.Download GraphSNP User Manual
Input file(s)
A multi-fasta SNP alignment
The alignment file must contain a minimum of two fasta-formatted nucleotide sequences of equal length.Download alignment example file
A distance matrix
Alternative to the alignment, a symmetric pairwise distance matrix can be used if users precompute the distance using 3rd party tools. The symmetric distance matrix should be written in CSV format.Download distance matrix example file
Metadata table
Metadata table must contain at least one non-empty column of sample_id. Sample identifier must be identical on both metadata and SNP alignment or matrix file. An additional column listing sample’s collection time (scaled in days, header: collection_day) is required for transmission analysisDownload metadata example file
Browser compatibility
GraphSNP was boostrapped using Create React App (CRA) tool and works on majority of modern browsers. GraphSNP was tested and compatible on the following browsers:- Microsoft Edge
- Chrome
- Firefox
- Opera
Core libraries
Thanks to all the frameworks and libraries run on the background, GraphSNP is now up and running and available worldwide. These are some of key frameworks and libraries used by GraphSNP:- React.js
- Data-Driven Documents (D3.js)
- Ant design UI
- Cytoscape
- Redux, bio-parsers, graphlib-dot, kruskal-mst, lodash, moment.
Have any questions?
Please feel free to send it to my email: b.permana@uq.edu.auRelated publications
- GraphSNP (available soon). In the meantime, please cite this website: https://graphsnp.beatsonlab.com
- CATHAI: cluster analysis tool for healthcare-associated infections