Building a reference database for metabarcoding and obitools
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2.6 years ago
beausoleilmo ▴ 490

I'm generating a reference database for metabarcoding of diet to find trnL markers (so looking at plants only).

I found the EMBL data that I was able to download using the following command

wget -P $EMBL -nH --cut-dirs=5 -A rel_std_pln_*.dat.gz -m ftp://ftp.ebi.ac.uk/pub/databases/embl/release/std/

Now I'd want to have other reference database and combine them using OBITools.

  1. What are the other public databases that I could use for plants? (like the NCBI taxonomy, GenBank, Barcode of Life DataSystems [BOLD], etc.)
  2. How to download them? Just for NCBI, I can't easily find how to download that
  3. How to merge databases in OBITools?
embl metabarcoding reference database plants diet • 1.1k views
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