Answers.Body: <p>I am not sure if I understand your first question correctly.</p>
  <p>Kraken is meant to be for the taxonomic classification of metagenomic sequencing data. Therefore, if you only have one target genome of interest there is no need to use Kraken. You can just use any sequence aligner and check the mapping rates.</p>
  <p>However, if you are trying to add a custom genome to an existing database then you need a taxonomy id for the sequence names in the genome and add it to your DB using the --add-to-library command. If this is what you are asking this tutorial would help you <a href="https://bioinformaticsworkbook.org/dataAnalysis/Metagenomics/Kraken.html#gsc.tab=0" rel="nofollow noreferrer">https://bioinformaticsworkbook.org/dataAnalysis/Metagenomics/Kraken.html#gsc.tab=0</a></p>
  <p>Regarding your second question, I truly believe those ref indexes are ready to go. You can download the tar file, extract it in a folder called MinusB and release the Kraken using, e.g., <code>kraken2 --db MinusB yourreads.fq</code></p>
  <p>Hope this helps</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-20T11:34:59.957Z
Answers.LastActivityDate: 2023-02-20T14:37:52.030Z
Answers.LastEditDate: 2023-02-20T14:37:52.030Z
Answers.UserDisplayName: CorteZero
Body: <p>I am attempting to build my own custom database for Kraken2. I have two questions:</p>
  <ol>
  <li>If I have the MCPyV genome in a file called MCPyV.fasta, how do I build a database with just this?</li>
  <li>How do I build the MinusB database? (<a href="https://benlangmead.github.io/aws-indexes/k2" rel="nofollow noreferrer">https://benlangmead.github.io/aws-indexes/k2</a>)</li>
  </ol>
  <p>For number one, I attempted to build this by using:</p>
  <pre><code>kraken2-build --add-to-library MCPyV.fasta --db my_db
  </code></pre>
  <p>But was returned an error stating that there was no taxonomy information found. How do I make this MCPyV.fasta file amenable to Kraken2 while building the database?</p>
  <p>For number 2, I again attempted to build the MinusB database using:</p>
  <pre><code>kraken2-build --build --threads 4 --db MinusB
  </code></pre>
  <p>and was returned an error regarding missing /taxonomy directory.</p>
  <p>Does anyone know how to build these databases properly?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T16:07:09.550Z
Comments.Text: Hi @interestingQuestion61 the answer is helpful (I use Kraken too), please consider upvoting/accepting.
Comments.UserDisplayName: M__
Tags: <phylogenetics><ngs><sequence-analysis><metagenome>
Title: How do I build the MinusB database for Kraken2? (Taxonomy issues)
ThreadText: # How do I build the MinusB database for Kraken2? (Taxonomy issues)
  
  (Asked by: username_0 on 2023-02-18)
  
  I am attempting to build my own custom database for Kraken2. I have two questions:
  
  1. If I have the MCPyV genome in a file called MCPyV.fasta, how do I build a database with just this?
  2. How do I build the MinusB database? (<https://benlangmead.github.io/aws-indexes/k2>)
  
  For number one, I attempted to build this by using:
  
  ```
  kraken2-build --add-to-library MCPyV.fasta --db my_db
  
  ```
  
  But was returned an error stating that there was no taxonomy information found. How do I make this MCPyV.fasta file amenable to Kraken2 while building the database?
  
  For number 2, I again attempted to build the MinusB database using:
  
  ```
  kraken2-build --build --threads 4 --db MinusB
  
  ```
  
  and was returned an error regarding missing /taxonomy directory.
  
  Does anyone know how to build these databases properly?
  
  **Tags:** phylogenetics, ngs, sequence-analysis, metagenome
  
  > **Comments:**
  > **username_1**: Hi @interestingQuestion61 the answer is helpful (I use Kraken too), please consider upvoting/accepting.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-02-20. Score: 1
  
  I am not sure if I understand your first question correctly.
  
  Kraken is meant to be for the taxonomic classification of metagenomic sequencing data. Therefore, if you only have one target genome of interest there is no need to use Kraken. You can just use any sequence aligner and check the mapping rates.
  
  However, if you are trying to add a custom genome to an existing database then you need a taxonomy id for the sequence names in the genome and add it to your DB using the --add-to-library command. If this is what you are asking this tutorial would help you <https://bioinformaticsworkbook.org/dataAnalysis/Metagenomics/Kraken.html#gsc.tab=0>
  
  Regarding your second question, I truly believe those ref indexes are ready to go. You can download the tar file, extract it in a folder called MinusB and release the Kraken using, e.g., `kraken2 --db MinusB yourreads.fq`
  
  Hope this helps
  
  
  ---
  
  