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README.md

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README

This repository contains the dataflow and scripts I used to process the COI metabarcode reads in the paper "Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators" in Scientific Reports.

If you use these data files or scripts in future work, please cite:

Porter, T.M., Morris, D.M., Basiliko, N., Hajibabaei, M., Doucet, D., Bowman, S., Emilson, E.J.S., Emilson, C.E., Chartrand, D., Wainio-Keizer, K., Séguin, A., Venier, L. 2019. Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators. Scientific Reports, 9: 18218. https://www.nature.com/articles/s41598-019-54532-0

Infiles

  1. The denoised ESV fasta files for the BE and F230 amplicons are in denoised_ESVs.fastas.zip

  2. The original taxonomic assignment matrix from the SCVUC bioinformatic pipeline is LV2016_1.tar.gz

  3. Sample x filename map GRDIname.map

  4. Taxonomic assignment matrix for ESVs with edited headers LV2016_2.tar.gz. Taxonomic assignment matrix for OTUs with edited headers LV2016_4.tar.gz.

  5. Metadata including latitude and longitude in metadata.csv

Scripts

  1. Raw reads were processed using the SCVUC v2.0 pipeline available from https://github.com/EcoBiomics-Zoobiome/SCVUC_COI_metabarcode_pipeline .

  2. The resulting taxonomic assignments for each marker were concatenated (LV2016_1.tar.gz) and headers edited for analysis in R (LV2016_2.tar.gz) using GRDIname.map and the Perl script reviseGRDInames2.plx .

  3. Figures were pepared in R as follows:

  • Fig 2 was generated with Fig2_Richness_FigS4_Venn_ESV_100919.R .
  • Fig 3 was generated with Fig3_BetaDiv_100819.R from LV2016_2.csv and metadata.csv .
  • Fig 4 was generated with Fig4_FigS7_FigS8_FigS9_indicator_heattree_ESV_100819.R .
  1. Supplementary figures were prepared in R as follows:
  • Fig S1 was generated with FigS1_phyla.R .
  • Fig S2 was generated with FigS2_PropConfID.R .
  • Fig S3 was generated with FigS3_Rarefaction.R .
  • Fig S4 was generated with Fig2_Richness_FigS4_Venn_ESV_100919.R .
  • Fig S5 was generated with FigS5_RichnessDNAextn.R .
  • Fig S6 was generated with FigS6_heatmap_indic_ESVs_100919.R
  • Fig S7, S8, S9 were generated with Fig4_FigS7_FigS8_FigS9_indicator_heattree_ESV_100819.R .

Acknowledgements

I would like to acknowledge funding from the Canadian government from the Genomics Research and Development Initiative (GRDI) Ecobiomics project.

Last updated: December 3, 2019