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title: "Using a Custom Kraken2 Database for Taxonomic Classification"
canonical: "https://help.biobam.com/space/OBD/3339124740/Using%20a%20Custom%20Kraken2%20Database%20for%20Taxonomic%20Classification"
format: markdown
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This describes how to upload and use a custom Kraken2 database for taxonomic classification in OmicsBox. Prerequisites:  Before you begin, please ensure the following: You have access to a custom Kraken2 database, consisting of three files (hash.k2d, taxo.k2d, opts.k2d). The Kraken2 database has been properly formatted and created from nucleotide sequence data, as OmicsBox does not accept raw data or protein-based databases. Ensure that your custom Kraken2 database is built using NCBI taxonomy; OmicsBox does not support Silva, Green Genes, or GTDB taxonomy databases. Procedure: Uploading a Custom Kraken2 Database Access the Cloud Files Tab: Open OmicsBox. On the left-hand side of the OmicsBox interface, you will find a panel with different tabs. Click on the "Cloud Files" tab to access your cloud storage. Create a New Folder and Name It: In the "Cloud Files" tab, navigate to the location where you want to upload your custom Kraken2 database. Right-click on the desired location, and a context menu will appear. Select "New Folder" from the context menu, and a new folder will be created. Name this folder as it will determine the database name in the OmicsBox user interface. Upload the Kraken2 Database Files: Locate the folder containing the three Kraken2 database files (hash.k2d, taxo.k2d, opts.k2d) on your local computer. Drag and drop all three database files into the newly created folder within the "Cloud Files" tab. Using the Custom Kraken2 Database for Taxonomic Classification To perform taxonomic classification using your custom Kraken2 database in OmicsBox, start going into the Taxonomic Classification dialog from the Metagenomics menu. Within the analysis settings, locate the "Database" drop-down control, click on it, and a list of available databases will appear. From this list, you will find your custom Kraken2 database, listed under the name of the folder where you placed the database files. Select your custom Kraken2 database by clicking on it. Once the custom database is selected, configure any additional parameters and settings specific to your taxonomic classification analysis. Finally, proceed with the taxonomic classification analysis following your typical workflow in OmicsBox. Figure 1:  How to set up and use a custom Kraken2 database.