Anacapa is an eDNA toolkit that allows users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data. It address longstanding needs of the eDNA for modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. Anacapa toolkit processes eDNA reads and assigns taxonomy using existing software or modifications to existing software. This modular toolkit is designed to analyze multiple samples and metabarcodes simultaneously from any Ilumina sequencing platform. A significant advantage of the Anacapa toolkit is that it does not require that paired reads overlap, or that both reads in a pair pass QC. Taxonomy results are generated for all read types and the user can decide which read types they wish to retain for downstream analysis. Check out the media coverage UCLA, MEE methods blogs, and Monga Bay.
Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.
Validating Taxonomic Assignments
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Thus we are in the process of developing tools to allow for metabarcode and reference database validation. For example, we recently evaluated the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Our results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts. Specifically, we employ a taxonomy cross-validation by identity framework to compare classification performance across classification parameters and reference databases. By combining CRUX with TAXXI researchers can validate any given metabarcodes of interest. We are currently developing these tools to allow for researchers to decide on the best metabarcoding loci for taxa of interest. Feel free to reach out if you are interest!