About this app and dataset

The San Francisco Bay HAB and phytoplankton community data presented here were obtained through 18s metabarcoding of surface water samples collected during bimonthly cruises aboard the USGS Peterson Cruises. Previous work on data processing and analysis conducted in collaboration with Keith Bouma-Gregson, USGS. See SFEI 2021 for further details on sample processing and analysis.

Classification pipeline is the product of an Anacapa-based workflow developed by Sean Jungbluth, SFSU (description of method in prep).

Pre-2022 data was sequenced via Illumina MiSEQ sequencers, while data from 2022-present was sequenced with NextSEQ, which has greater sensitivity and sequencing depth.

More information on general sequencing approach can be found in Nardelli et al., 2026 and Killam et al., 2026. Note that both papers use pipelines that have been superceded by the approach of this Shiny app.

Raw sequencing data available on NCBI, and past classified phytoplankton data available on EDI.

This Shiny application is the result of a collaboration between the San Francisco Estuary Institute Nutrient Management Strategy,USGS California Water Science Center, Bend Genetics, and the UCSC Kudela Lab.

Questions about the app can be sent to Dan Killam at SFEI.