NCBI or SILVA for curating a custom 16S rDNA reference database?

General Discussion
2

Hi @deClare125,

There are several ways you can go about this...

  1. For Eukaryotic specific reference sequences, you can try
    • get-eukaryome-data: use SSU to grab 16S rRNA gene data.
    • get-midori2-data: to grab mitochondrial reference data. Use srRNA for the 16S rRNA gene data, and CO1 for cytochrome oxidase subunit 1 data.
  2. Then, if you'd like, you can follow the extract-seq-seqments tutorial using these reference databases.

^^Note: the online documentation does not appear to reflect the current database options for these commands. So, be sure to check out the respective options using the --help flag.

I've not tested this, but given that you are are performing an eDNA diet survey, I am thinking that these two databases might be better tailored for assessing diet eDNA. Then you can use GTDB, SILVA, and Greengenes 2 to assess microbial diversity.

For the NCBI query, I'd try and limit it to non-microbial data using the taxonomy ID to restrict which taxonomic groups you like to keep or ignore. But I think the two databases I mentioned above have already done much of the hard work for you. So, give those a try and see how they work for you.

If you go with using get-silva-data I'd follow the initial steps to fetch the data from here, through reverse transcribing, then you can use either feature-classifier extract-reads alone, or work through the extract-seq-segments tutorial.

Please update us on how well these work! :slight_smile:

-Mike

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extract-seq-segments: number of reads vs accuracy of reads.