> For the complete documentation index, see [llms.txt](https://help.dragen.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-db.md). # 16S Pipeline Pre-Built Database The 16S pipeline depends on a k-mer database of 16S reference sequences. The user can provide [a FASTA file](/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-custom-db.md) with reference sequences for a database to be built on the fly during the analysis. Or, the pre-built Refseq-RDP-v1 database can be used. ## Refseq-RDP-v1 Description The [Refseq-RDP-v1](https://zenodo.org/records/2541239) database contains 14,676 bacterial & 660 archaeal full-length 16S rRNA gene sequences. It was compiled in 14/05/2018 from predominantly the [NCBI RefSeq 16S rRNA database](https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) and was supplemented with extra sequences from the RDP database. The same 16S sequence content was used to build the default 16S database provided with the 16S Metagenomics v1.1.3 app (RefSeq RDP 16S v3 May 2018 DADA2 32 bp). Citation: Ali Alishum. (2019). DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea (Version 1) \[Data set]. Zenodo. ## Downloading the Database The database is free to download via a shell script using the instructions below. ### (1) Create a directory that will be dedicated to storing the database files It is recommended that the directory be on a disk with at least 1 GB of free space. The path to this directory will be used for the `-d` parameter when the download script is run in subsequent steps. In the example commands below, the directory is named "databases". ``` mkdir databases ``` ### (2) Download the shell script Download the shell script and make it executable: ``` wget -O explify-dbs.sh https://illumina-explify-databases.s3.us-east-1.amazonaws.com/explify-dbs.sh chmod +x explify-dbs.sh ``` ### (3) View the database versions that are available for download ``` ./explify-dbs.sh search -d databases/ -p Refseq-RDP-v1 ``` The command will print the available databases, e.g.: ``` 1 database(s) found meeting those criteria: - Refseq-RDP-v1-1.0.1 ``` ### (4) Download the database ``` ./explify-dbs.sh download -d databases/ -p Refseq-RDP-v1 -v 1.0.1 -n 20 ``` * The `-v` argument is the database version observed in step 3 * The `-n` argument is the number of CPUs that can be used to download the files (defaults to 1) Additional notes: * In this example, after the Refseq-RDP-v1-1.0.1 files are downloaded, additional required files will be downloaded to a subdirectory named "common" * After the files are downloaded, their checksums will be automatically checked ### (5) Use the database in an analysis The database files will have been downloaded to `databases/Refseq-RDP-v1/1.0.1/`. This path is then used with the `--16s-db-dir` command line argument. ### Verifying the Downloaded Files The checksums of the individual database files are verified automatically as part of the `download` command, but they can also be verified at any later time with the `check` command: ``` $ ./explify-dbs.sh check -d databases/ -p Refseq-RDP-v1 -v 1.0.1 -n 20 ``` --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-db.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.