Rapid exploration and visualization through an automated metabarcoding pipeline

The revolution and acceleration in DNA sequencing over the past three decades has driven the development of new biomolecular tools like environmental DNA (eDNA) metabarcoding for characterizing marine biodiversity. In order to operationalize eDNA approaches for routine NOAA observatories, new bioinformatic programs and improved organismal reference barcodes are needed to provide accurate and reliable biological data in a timely manner. To address these needs, we present Rapid Exploration and Visualization through an Automated Metabarcoding Pipeline (REVAMP), which provides streamlined end-to-end data processing from raw reads to data exploration, visualization, and hypothesis generation. One benefit of REVAMP is the ability to iteratively assess marker gene and reference database performance. Here, we used a filtered reference database that only included sequences uploaded prior to specified date cutoffs from 1995 to 2022 to analyze changes in eDNA metabarcoding taxonomic assignments, revealing patterns of uneven improvement in taxonomic assignment depth and accuracy across time, region, and marker sets. This work highlights the need for targeted reference sequencing efforts for key regional taxa and the importance of such efforts for improving eDNA biomonitoring approaches in the future.