hajibabaei-lab / hajibabaeietal2019

Datasets and code used to create figures in "Hajibabaei et al., 2019. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS ONE 14(9): e0220953."

README

This repository contains the datasets and scripts used to create the figures in:

Hajibabaei et al., 2019. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS ONE 14(9): e0220953.

Data analysis outline

1. Raw reads are available from the NCBI SRA # PRJNA545426 and were processed using the SCVUC v2.1 pipeline available from https://github.com/EcoBiomics-Zoobiome/SCVUC_COI_metabarcode_pipeline .

2. Datasets: The taxonomic assignments are available in taxonomy.matrix.gz . Site locations are in Sites.csv . FASTA files for the denoised ESVs are in denoised_ESVs_supmat.tar.gz .

3. Figures were pepared in R as follows:

• Fig 2 was generated with Fig2_multimarker_richness_accumulation.R from taxonomy.matrix.gz .
• Fig 3 was generated with Fig3_site_waterquality_indicators.R from taxonomy.matrix.gz .
• Fig 4 was generated with Fig4_site_indicator_species_heatmap.R from taxonomy.matrix.gz. Final editing was done in Inkscape.
• Fig 5 was generated with Fig5_NMDS.R from taxonomy.matrix.gz .

4. Supplementary figures were prepared in R as follows:

• Fig S1 was generated with FigS1_map.R from Sites.csv .
• Fig S2 was generated with FigS2_TaxSummary.R from taxonomy.matrix.gz .
• Fig S3 was generated with FigS3_rarefaction.R from taxonomy.matrix.gz .
• Fig S4 was generated with FigS4_MedianRichness.R from taxonomy.matrix.gz .
• Fig S5 was generated with FigS5_TotalRichness.R from taxonomy.matrix.gz .

Acknowledgements

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

Last updated: Sept. 9, 2019.