DOI: 10.5061/dryad.mf0126f
title: Data from: Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

description: 1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor
 species and community diversity that is rapid, affordable, and
 non-invasive. Longstanding needs of the eDNA community are modular
 informatics tools, comprehensive and customizable reference databases,
 flexibility across high-throughput sequencing platforms, fast multilocus
 metabarcode processing, and accurate taxonomic assignment. As
 bioinformatics tools continue to improve, addressing each of these demands
 within a single bioinformatics toolkit is becoming a reality. 2. Here we
 present an open access modular metabarcode sequence toolkit, Anacapa
 (https://github.com/limey-bean/Anacapa/), that addresses the above needs,
 allowing users to build comprehensive reference databases and process raw
 multilocus metabarcode sequence data to accurately characterize
 communities. A novel aspect of Anacapa is our database builder, Creating
 Reference libraries Using eXisting tools (CRUX), that generates
 comprehensive reference databases for specific user-defined metabarcode
 loci. The Quality Control and Dereplication module sorts and processes
 multiple metabarcode loci and processe merged, unmerged and unpaired reads
 maximizing recovered diversity. Next DADA2 detects amplicon sequence
 variants (ASVs) and the Anacapa Classifier module aligns these ASVs to
 CRUX-generated reference databases using Bowtie2. Taxonomy is assigned to
 ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA)
 method. The Anacapa toolkit also includes an R package, ranacapa, for
 automated results exploration through standard biodiversity statistical
 analysis. 3. Comparative tests to other published reference databases show
 that CRUX generates broad, comprehensive reference databases that capture
 more taxonomic diversity. A variety of benchmarking approaches show that
 the Anacapa Classifier module’s Bowtie2-BLCA assigns robust, high-quality
 taxonomy to both MiSeq and HiSeq-length eDNA metabarcode sequences. We
 further demonstrate the utility of the Anacapa Toolkit by assigning
 taxonomy to eDNA sequences from terrestrial and marine samples from
 southern California through CaleDNA (http://www.ucedna.com/). 4. The
 Anacapa Toolkit broadens the exploration of eDNA and assists in
 biodiversity assessment and management by generating metabarcode specific
 databases, processing multilocus data, retaining all read types, and
 expanding non-traditional eDNA targets. Anacapa software and source code
 are open and available in a virtual container to ease installation.
description: CRUX-CO1Filtered CRUX-CO1 reference databaseCO1.zipCRUX-FITSFiltered CRUX-FITS (fungal its) reference databaseFITS.zipCRUX-PITSFiltered CRUX-PITS (Plant ITS2) reference databasePITS.zipCRUX-16SFiltered CRUX-16S reference database16S.zipCRUX_18SFiltered CRUX_18S reference database18S.zipCRUX_12SFiltered CRUX_12S reference database12S.zipCRUX_V8-9_18SFiltered CRUX_V8-9_18S reference databaseV8-9_18S.zipCRUX_V4_18SFiltered CRUX_V4_18S reference databaseV4_18S.zipAnacapahttps://github.com/limey-bean/Anacapa as of 5-10-2019CRUX_Creating-Reference-libraries-Using-eXisting-toolshttps://github.com/limey-bean/CRUX_Creating-Reference-libraries-Using-eXisting-tools as of 5-10-2019R-P-HCRUX length Restricted Porter & Hajibabaei CO1 databaseR-mitofishCRUX length restricted mitofish reference databaseR-MidoriCRUX length restricted Midori reference databaseR-CO-ARBitratorCRUX length restricted CO-ARBitrator reference databaseR_UNITECRUX length restricted UNITE reference databaseR-WITSCRUX length restricted WITS reference database