Answers.Body: <p>\$DBNAME is a folder location on your computer; you specify it yourself, for example:</p>
  <pre><code>kraken2-build --standard --db /media/ip80/externalDrive/kraken_indexes/betterThanGenbank
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-18T19:54:56.220Z
Answers.LastActivityDate: 2023-02-18T19:54:56.220Z
Answers.UserDisplayName: gringer
Body: <p>I am at this point in the GitHub tutorial: <a href="https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#standard-kraken-2-database" rel="nofollow noreferrer">https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#standard-kraken-2-database</a></p>
  <p>It says to create the standard Kraken database, I use the following command:</p>
  <pre><code>kraken2-build --standard --db $DBNAME
  </code></pre>
  <p>It then says to change <code>$DBNAME</code> with the preferred database name/location. Is this something that I need to download on my own? Where can I find it, and how do I do it?</p>
  <p>To provide context, I want to use Kraken2 to identify whether or not there is the presence of MCPyV in a tumor sample.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-18T10:58:45.520Z
Comments.Text: If you just want the viral database, read the 'custom databases' section (https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases)
Comments.UserDisplayName: jared_mamrot
Tags: <ngs><linux><metagenome>
Title: How do I build the "Standard Kraken 2 Database"?
ThreadText: # How do I build the "Standard Kraken 2 Database"?
  
  (Asked by: username_0 on 2023-02-18)
  
  I am at this point in the GitHub tutorial: <https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#standard-kraken-2-database>
  
  It says to create the standard Kraken database, I use the following command:
  
  ```
  kraken2-build --standard --db $DBNAME
  
  ```
  
  It then says to change `$DBNAME` with the preferred database name/location. Is this something that I need to download on my own? Where can I find it, and how do I do it?
  
  To provide context, I want to use Kraken2 to identify whether or not there is the presence of MCPyV in a tumor sample.
  
  **Tags:** ngs, linux, metagenome
  
  > **Comments:**
  > **username_1**: If you just want the viral database, read the 'custom databases' section (https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-02-18. Score: 2
  
  \$DBNAME is a folder location on your computer; you specify it yourself, for example:
  
  ```
  kraken2-build --standard --db /media/ip80/externalDrive/kraken_indexes/betterThanGenbank
  
  ```
  
  
  ---
  
  