SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent‐coverage threshold to filter out false positives, (b) an internal‐standard DNA spike‐in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental‐sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, spec...,
ArcDyn_tutorial_20190126.tar.gz
Text S6. How to run Step 4 (bioinformatics) of the SPIKEPIPE pipeline. Here we describe how to the user may apply SPIKEPIPE pipeline to a subset of the data used in this paper, henceforth called ArcDyn tutorial. To install the ArcDyn tutorial, download and untar the 4.9 GB tutorial file (ArcDyn_tutorial_20190126.tar.gz) to the root directory.
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