Info-Fish: Matching eDNA Recovered Species to Ecological Information from Fishbase

eDNA is a unique tool to accurately and rapidly assess marine biodiversity (Taberlet et al. 2012). However, there are still several challenges that prevent widespread eDNA use. For example, accurate species assignment and assigning species recovered from eDNA to relevant ecological information present two challenges to implementing eDNA monitoring assessments. To address the first problem, Curd et al. created a bioinformatics pipeline to parse amplicon sequence variants (ASVs) and assign taxonomy to sequences (Curd et al. 2019). The outputs of the Anacapa pipeline are species tables with bootstrapped confidence scores. The goal of this project is to take the Anacapa output .txt file and match the recovered species to their respective trait data. Trait data is obtained from FishBase, an online database of information of fish and elasmobranchs ecology such as habitat, diet, fecundity, and distribution (Froese and Pauly, 2019). This program is constructed in R and uses the package rfishbase to match species to trait data (R Core Team 2018; Boettiger et al. 2012). Github link: https://github.com/ksmonuki/info-fish