A WebAssembly implementation of the HIV-TRACE pipeline.
Uses cawlign, tn93, hivcluster-rs, and hivannotate-rs. Implemented using Biowasm and WebAssembly.
- HIV-TRACE Pipeline: Complete end-to-end sequence analysis in the browser
- Reference Selection: Choose from multiple references or upload custom reference sequences
- Network Annotation: Annotate network nodes with patient attributes and metadata
- Customizable Parameters: Adjust distance threshold, overlap, and other pipeline parameters
- Downloadable Results: Get results in JSON, FASTA, and CSV formats for further analysis
- Python Implementation: For the original Python implementation of HIV-TRACE, visit github.com/veg/hivtrace
- AUTO-TUNE: A tool for selecting the optimal distance threshold for HIV transmission clusters available at autotune.datamonkey.org
- Reference: Weaver S, Dávila Conn VM, Ji D, Verdonk H, Ávila-Ríos S, Leigh Brown AJ, Wertheim JO and Kosakovsky Pond SL (2024) AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters. Front. Bioinform. 4:1400003. doi: 10.3389/fbinf.2024.1400003
- COVFEFE: A tool for evaluating HIV genetic networks at covfefe.datamonkey.org