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eDNA results 🐠

This is a workflow for processing eDNA results from the eDNA Expeditions project into an integrated dataset. Source data are fetched from AWS and edna-tracker-data.

Steps:

  • Fetch metadata from GitHub
  • Fetch pipeline results from AWS
  • Combine data by site
  • WoRMS matching and taxonomy replacement
  • Separate blanks data
  • Apply annotations (remove or update names)
  • Generate WoRMS aligned species lists and statistics
  • Upload results to AWS

How to use this dataset

Download the dataset

Download the zipped dataset from https://obis-edna-results.s3.amazonaws.com/output.zip and extract.

rm -r output output.zip
wget https://obis-edna-results.s3.amazonaws.com/output.zip
unzip output.zip

Read the dataset using R

See https://github.com/iobis/edna-results/blob/master/docs/read.md.

Access species lists

This package also outputs species lists, download from https://obis-edna-lists.s3.amazonaws.com/output_lists.zip or browse the lists here.