Answers.Body: <p>The core idea behind BUSCO is that there are a number of genes that are Unique Single-Copy Orthologues (USCOs) that should be present in most genomes and should only appear <em>once</em> in the genome. This is only a guess, however, and not a universal rule.</p>
  <p>Sometimes genomes can have multiple copies of these USCOs, and these duplicated genes reduce the overall score (which is based on the proportion of complete <em>single-copy</em> genes that are present as a fraction of the entire USCO set).</p>
  <p>Regarding human DNA, bacteria are a curiously diverse group, with genomes that have more similarities in function than in form. Given this diversity, it wouldn't surprise me if contaminating DNA could increase the BUSCO score.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-01T18:59:11.800Z
Answers.LastActivityDate: 2021-11-02T21:05:57.510Z
Answers.LastEditDate: 2021-11-02T21:05:57.510Z
Answers.UserDisplayName: gringer
Body: <p>I have two assemblies obtained from two different softwares for the same run data. In one of them, I get a BUSCO score of 69,4%. In the other one, I get 68,5%. The first assembly covers a 99,7% fraction of the reference while the second one covers 100%.</p>
  <p>The relevant thing is that the reference genome also gets 68,5% (less than the first assembly). How can I interpret this situation?</p>
  <p>I identify these options:</p>
  <ul>
  <li>The first assembly is showing a different strain.</li>
  <li>BUSCO is imprecise</li>
  <li>The first assembly is merging DNA from another organism</li>
  <li>The first assembly is a misassembly, repeating part of the sequence and BUSCO interprets that as new genes</li>
  <li>The sample really is an organism that has more genes than the reference.</li>
  </ul>
  <p>The organism is a bacteria and I am using bacteria_odb10 as the lineage dataset.</p>
  <p>This is the BUSCO result for the reference (LN554883.1 Chlamydophila abortus strain 1H):</p>
  <pre><code>C:68.5%[S:68.5%,D:0.0%],F:8.1%,M:23.4%,n:124       
  85  Complete BUSCOs (C)            
  85  Complete and single-copy BUSCOs (S)    
  0   Complete and duplicated BUSCOs (D)     
  10  Fragmented BUSCOs (F)              
  29  Missing BUSCOs (M)             
  124 Total BUSCO groups searched
  </code></pre>
  <p>This for the first assembly:</p>
  <pre><code>C:69.4%[S:69.4%,D:0.0%],F:8.9%,M:21.7%,n:124       
  86  Complete BUSCOs (C)            
  86  Complete and single-copy BUSCOs (S)    
  0   Complete and duplicated BUSCOs (D)     
  11  Fragmented BUSCOs (F)              
  27  Missing BUSCOs (M)             
  124 Total BUSCO groups searched     
  </code></pre>
  <p>And this for the second assembly:</p>
  <pre><code>C:68.5%[S:0.0%,D:68.5%],F:8.1%,M:23.4%,n:124       
  85  Complete BUSCOs (C)            
  0   Complete and single-copy BUSCOs (S)    
  85  Complete and duplicated BUSCOs (D)     
  10  Fragmented BUSCOs (F)              
  29  Missing BUSCOs (M)             
  124 Total BUSCO groups searched
  </code></pre>
  <p>I see now that the first assembly also contains a lot of contigs with human DNA. I guess BUSCO finds a match for some genes in the human DNA?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-11-02T11:06:13.917Z
Comments.Text: I see now that the first assembly also contains a lot of contigs with human DNA. I guess BUSCO finds a match for some genes in the human DNA?
Comments.UserDisplayName: juanjo75es
Tags: <assembly><busco>
Title: BUSCO results apparently inconsistent
ThreadText: # BUSCO results apparently inconsistent
  
  (Asked by: username_0 on 2021-11-01)
  
  I have two assemblies obtained from two different softwares for the same run data. In one of them, I get a BUSCO score of 69,4%. In the other one, I get 68,5%. The first assembly covers a 99,7% fraction of the reference while the second one covers 100%.
  
  The relevant thing is that the reference genome also gets 68,5% (less than the first assembly). How can I interpret this situation?
  
  I identify these options:
  
  * The first assembly is showing a different strain.
  * BUSCO is imprecise
  * The first assembly is merging DNA from another organism
  * The first assembly is a misassembly, repeating part of the sequence and BUSCO interprets that as new genes
  * The sample really is an organism that has more genes than the reference.
  
  The organism is a bacteria and I am using bacteria\_odb10 as the lineage dataset.
  
  This is the BUSCO result for the reference (LN554883.1 Chlamydophila abortus strain 1H):
  
  ```
  C:68.5%[S:68.5%,D:0.0%],F:8.1%,M:23.4%,n:124       
  85  Complete BUSCOs (C)            
  85  Complete and single-copy BUSCOs (S)    
  0   Complete and duplicated BUSCOs (D)     
  10  Fragmented BUSCOs (F)              
  29  Missing BUSCOs (M)             
  124 Total BUSCO groups searched
  
  ```
  
  This for the first assembly:
  
  ```
  C:69.4%[S:69.4%,D:0.0%],F:8.9%,M:21.7%,n:124       
  86  Complete BUSCOs (C)            
  86  Complete and single-copy BUSCOs (S)    
  0   Complete and duplicated BUSCOs (D)     
  11  Fragmented BUSCOs (F)              
  27  Missing BUSCOs (M)             
  124 Total BUSCO groups searched     
  
  ```
  
  And this for the second assembly:
  
  ```
  C:68.5%[S:0.0%,D:68.5%],F:8.1%,M:23.4%,n:124       
  85  Complete BUSCOs (C)            
  0   Complete and single-copy BUSCOs (S)    
  85  Complete and duplicated BUSCOs (D)     
  10  Fragmented BUSCOs (F)              
  29  Missing BUSCOs (M)             
  124 Total BUSCO groups searched
  
  ```
  
  I see now that the first assembly also contains a lot of contigs with human DNA. I guess BUSCO finds a match for some genes in the human DNA?
  
  **Tags:** assembly, busco
  
  > **Comments:**
  > **username_0**: I see now that the first assembly also contains a lot of contigs with human DNA. I guess BUSCO finds a match for some genes in the human DNA?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-11-01. Score: 1
  
  The core idea behind BUSCO is that there are a number of genes that are Unique Single-Copy Orthologues (USCOs) that should be present in most genomes and should only appear *once* in the genome. This is only a guess, however, and not a universal rule.
  
  Sometimes genomes can have multiple copies of these USCOs, and these duplicated genes reduce the overall score (which is based on the proportion of complete *single-copy* genes that are present as a fraction of the entire USCO set).
  
  Regarding human DNA, bacteria are a curiously diverse group, with genomes that have more similarities in function than in form. Given this diversity, it wouldn't surprise me if contaminating DNA could increase the BUSCO score.
  
  
  ---
  
  