515F-Y_926R_database_construction

This is a repository that shows the steps for creating qiime2 classifiers specific for the "Parada primers". You might find yourself needing to do this when updating qiime2 as the scikit-learn version used to create the classifer needs to be the same as your version of qiime2. Selected artifacts are available at the OSF.io link below. Please open a github issue if you have any questions. If you want to add other artifacts to the OSF repo, you can just make a free account on OSF and ask to collaborate.

How artifacts were created:

1. Using the steps outlined in the RESCRIPt tutorial posted on the qiime2 forum (see link below), SILVA (138.1) classifiers were created for the 515F-Y / 926R primers.
2. The dereplicated sequences and taxonomy were exported to create input files for VSEARCH.
3. These files were formatted to the requirements of the SINTAX algorithm (see VSEARCH manual) using a custom python script.
4. A UDB file was then created with VSEARCH.
5. For PR2 (4.14.0), the "UTAX" file was downloaded and directly converted to a UDB file for VSEARCH without any further QC.
6. To train the PR2 classifier for qiime2, the steps for SILVA were followed except no length-based filtering was applied.
7. All four classifiers were uploaded to OSF.io.

To do:

• Re-jig pipeline to include updated db and new workflow (PR2 as first-pass, SILVA138.1 second)

Location of finished artifacts:

https://osf.io/e65rs/

Source for RESCRIPt commands: https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494

Source for PR2 files: https://github.com/pr2database/pr2database/releases/tag/v4.14.0