Methods in Marine Biodiversity

This is a collection of files for the Marine Biodiversity Methods course at Friday Habor Labs.

Methods

Taxonomic Annotation

We applied a number of quality filters to the sequence data (everything up to pre-clustering); now the aim is to apply a taxon name to each sequence.

Our approach for taxonomic annotation is the following:

• Does the sequence have a match in the FHL course barcode database at >97% identity? (blastn)
  • YES:
    • Is there only one hit at that level?
      • YES: use the name associated with that specimen
      • NO: use multiple names, resolving differences by (???...???)
  • NO:
    • Does the sequence match a sequence in GenBank at >97% identity? (blastn)
      • YES:
        • Is there only one hit at that level?
          • YES: use the name associated with that specimen
          • NO: use multiple names, resolving differences by (???...???)
      • NO:
        • After clustering at 5% (CROP), does OTU sequence have a match in GenBank at >85% identity? (blastn)
          • YES: use the phylum name associated with that GenBank sequence
          • NO:
            • Does the sequence have a probability of assignment to a sequence in (database?) with posterior probability >0.8?
              • YES: use the phylum name associated with that taxon
              • NO: sequence is labeled as 'unidentified taxon'

The output of this process is a table with the following columns; one row for each sequence in the pre-clustering fasta file:

• seq_id [char]: sequence header from pre-clustering fasta file
• FHL_db [boolean]: hit in local database?
• GB_95 [boolean]: hit in GenBank >95%id?
• CROP_ID [char]: sequence header of the OTU fasta file
• GB_85 [boolean]: hit in GenBank >85%id after clustering?
• SAP_prob [numeric,{0,1}]: posterior probability of assignment to a taxon using SAP
• taxon_name [char]: taxon name