ON-Time
From rectal swab to a clinically actionable gut microbiome result in under five hours
ON-Time transforms a single rectal swab into a clinically actionable gut microbiome profile in less than five hours, enabling timely decision-making in the intensive care unit (ICU). In contrast, conventional 16S rRNA sequencing and shotgun metagenomic workflows typically require several days to weeks before results are available.
- ~1.75 h — DNA extraction and library preparation
- ~3 h — Sequencing on an Oxford Nanopore MinION Mk1B using a Flongle flow cell
- Real time — Taxonomic classification as sequencing reads accumulate
ON-Time provides the final, point-and-click analysis step. Simply upload Kraken reports generated by the EPI2ME wf-metagenomics workflow for a patient sample together with its matched negative control. ON-Time automatically removes contaminant taxa, restricts the analysis to bacterial communities, and generates an interpretable clinical summary, including:
- Shannon diversity index
- Whether Enterobacteriaceae is the dominant bacterial family
- An overall infection risk assessment
Run locally
Want to keep patient data local? ON-Time is published as a public Docker image, so you can run the exact same app on your own computer. Everything stays on your machine — nothing is uploaded.
Install Docker, then run:
Then open http://localhost:11631 in your browser.
Citation
If you use ON-Time in your work, please cite:
MacKenzie C, Seo H, Schlechte J, Herik A, Bains I, Yu I-L, McCoy KD, Thornton CS, McDonald B. ON-Time: rapid microbiome sequencing and analysis for precision medicine. In press.