This repository contains the dataflow and scripts used to process the COI metabarcode reads in the paper Robinson et al., 2020.
Infiles, R scripts, and supplementary data files can be downloaded from https://github.com/terrimporter/RobinsonEtAl2020/releases .
cat.csv contains the ESV ids, sample names, and taxonomic assignments.
Values_for_VennDiagrams.xlsx contains the values used in the Venn diagrams.
Sites.csv contains the coordinates needed to plot sites on the map.
Fig1_Richness.R calcualtes ESV richness. Uses cat.csv as an infile.
Fig2_NMDS.R creates NMDS plots. Uses cat.csv as an infile.
Fig3_Venn.R draws Venn diagrams. Uses values from Values_for_VennDiagrams.xlsx
Fig4_AntifreezeVsEthanol.R compares Ethanol vs Antifreeze xy-plot showing orders and genera. Uses cat.csv as an infile.
Fig5_EPTheatmap.R compares Ethanol vs Antifreeze EPT families as heatmaps. Uses cat.csv as an infile.
FigS1_Map.R plots sites on the map. Uses Sites.csv as an infile.
FigS3_Phyla_SuppTable.R plots the read abundance for each phylum. Uses cat.csv as an infile.
FigS4_Rarefaction.R plots rarefaction curves. Uses cat.csv as an infile.
FigS5_PropConf.R plots the number of unique taxa, all versus those confidently identified. Uses cat.csv as an infile.
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Denoised, chimera-filtered ESVs (FASTA) for BR5, F230R, and ml-jg.
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Denoised, chimera-filtered ESVs, pseudogene-filtered ORFs (FASTA) for BR5, F230R, and ml-jg.
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ESV x sample tables for BR5, F230R, and ml-jg. These are based on the denoised, chimera-, and pseudogene-filtered ESVs.
Robinson, C.V., Porter, T.M., Wright, M.T., Hajibabaei, M. (2020) Propylene glycol-based antifreeze is an effective preservative for DNA metabarcoding of benthic arthropods. Freshwater Science, 40(1): 77-87. https://www.journals.uchicago.edu/doi/full/10.1086/712232
I would like to acknowledge funding from the Canadian government from the Genomics Research and Development Initiative (GRDI), Metagenomics-Based Ecosystem Biomonitoring (Ecobiomics) project.
Last updated: Nov. 10, 2021