16Sguild Database

This app processes ASVs from your 16S data, filters unreliable sequences, and assigns each ASV a universal unique identifier (UUID). These UUIDs allow microbial features (amplicon sequencing variants, or ASVs) to be consistently tracked across datasets and studies, enabling reproducible and comparable microbiome analyses. Users will receive a linkage table that contains UUIDs for the ASVs submitted.

How to Use

• Upload your RDS bundle from the 16Sguild pipeline. This bundle will contain ASV sequences (FASTA format), feature table (ASV x sample abundance matrix), and ASV filtering cutoff parameters (as defined in params.yml).
• Fill in the Base Name, Contact Name, and Contact Email. Please be as specific as possible.
• Base Name should be populated with the same value as used in base_name for the params.yml file.
• Contact Name and Contact Email are only required to help keep track of the database submissions in case the submission needs to be altered.
• Test Mode:
• If you are using the NYU example dataset, select the 'test' option. This will automatically populate 'Base Name', 'Sequencing Platform', and '16S rRNA Region'.
• Please enter your contact name and email.
• Select the Sequencing Platform and 16S rRNA Region.
• Acknowledge that you understand the database contribution.
• Click 'Run Filtering' to process sequences and generate ASV UUIDs.
• After processing, results will be available in three tabs:
• Feature Table: Your filtered ASV abundance table.
• Assigned ASVs: ASVs with their corresponding UUIDs.
• Database Submission: Indicates which ASVs are new to the database vs already existing.
• Download the ASV linkage table. This table could be uploaded into the 16Sguild pipeline as 'linkage_table'.

Notes & Tips

• Ensure your sequences in the FASTA file match the feature table.
• The ASV UUID assignment ensures no duplicates in the database. This can be viewed under the 'Database Submission' tab. The new ASVs will be listed under 'New ASVs'.
• If no new ASVs are found, your data will still receive UUID assignments and a fully populated linkage table. In this case, no additional entries will be added to the UUID database.
• All logs in the console help track progress or errors.

Contact

For questions or troubleshooting, leave a comment in the Issues section of the GitHub repository.