About Phage Annotation Server
Phage Annotation Server is a free public service that runs the pharokka → phold → phynteny phage annotation pipeline on uploaded genomes: gene calling, structure-guided functional annotation, and synteny-based completion of remaining unknown genes, presented as one coherent results page instead of three separate tool outputs.
Research use only
Results, including antimicrobial-resistance (CARD) and virulence-factor (VFDB) hits reported by pharokka, are provided for research purposes only. They are not validated for, and must not be used for, clinical or diagnostic decision-making.
How to cite
If this service was useful for your work, please cite pharokka, phold and phynteny individually -- each tool's own repository documents the current, correct citation. See the citation page for full references and copyable BibTeX.
What we store, and for how long
- Your uploaded sequence is rewritten into a canonical FASTA before any processing touches it; original contig names are kept only in a small mapping file used to redisplay them to you.
- The submitting IP address is retained for abuse prevention and usage statistics (rate limiting, and an internal, non-public view of how the service is being used) -- it is never published or shared. It is deleted along with the rest of the job's data at the end of the retention window below.
- An email address is stored only if you provide one, solely to share your results link. It is never used for anything else, and is deleted along with the job.
- Job inputs and outputs are kept for 30 days after submission, then permanently deleted. Download your results before then if you want to keep them.
Abuse prevention
Submissions are rate-limited per IP address, and inputs are size-, contig-count- and complexity-capped before a job is ever queued. The raw file you upload is never served back by this site -- only files generated by the pipeline itself.
Compute
Jobs run CPU-only, with a per-job time limit, so one submission can't starve the queue for everyone else.
Software versions
This deployment is currently running:
- pharokka 1.10.1
- phold 1.3.0
- phynteny_transformer 0.1.3
Contact
For questions, bug reports, or takedown requests, get in touch with George Bouras: george.bouras [at] adelaide.edu.au, or via the project's source code repository.