Sharing Data
In our work comparing different approaches to pathogen detection and piloting a biosurveillance system, we collect metagenomic sequencing data. We aim to share as much of this data as we can, while respecting access restrictions requested by our partners.
Zephyr (Boston Nasal Swabs)
We collect nasal swabs at public locations in greater Boston. Sequences we identify as potentially human-infecting viruses are linked from our sample log in FASTQ format. We have also published our data via the SRA (PRJNA1379685).
CASPER (Wastewater Sequencing)
In collaboration with Marc Johnson’s group at the University of Missouri, we are monitoring wastewater from multiple metropolitan areas. We have a dashboard tracking pathogen abundance over time.
As of May 2025, we have sequenced 368B read pairs from December 2023 onward and are adding roughly 35B read pairs per week. 170B read pairs from Boston, Chicago, and Riverside are available on the SRA (PRJNA1247874). If you would like access to data that has not yet been made public, please send us a brief description of your research.
In collaboration with Jason Rothman and Katrine Whiteson’s lab at UC Irvine/Riverside, we sequenced wastewater from Los Angeles. This work has a preprint on SSRN and 45B read pairs are available on the SRA (PRJNA1198001).