Data from: Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

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.