Manually Adding Positive Controls to classifier or reference database

General Discussion
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I'm wondering if there is an easy way to add sequences/taxonomy to a reference database created with QIIME.

I'm working on an eDNA metabarcoding project and want to detect species not present on NCBI's GenBank database. I have tissue samples from those species, and can thus sequence them with the same metabarcoding primers that I'm using for my study.

I would either Sanger sequence them with the metabarcoding primers, or would sequence them on the Illumina platform, then get a consensus sequence for that individual (although that seems a bit overkill).

I could add these directly to GenBank, then use rescript get-ncbi-data to download them in the proper format. Instead, I'm wondering if there's an easy way to manually add them instead.

Thanks for your help! I'd love to know if there is a standard procedure for this.

2

Hi @alexkrohn ,

  1. Use rescript to download your database etc
  2. import your new sequences and taxonomy as FeatureData[Sequence] and FeatureData[Taxonomy]
  3. use qiime feature-table merge-seqs to add the new sequences to your database
  4. use qiime feature-table merge-taxa to add the new taxonomies to your database (rescript also has a merge-taxa action that could be used for this, but that is for a more advanced case).

Good luck!

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