<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>

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2021-11-01T18:59:11.800Z
2021-11-02T21:05:57.510Z
2021-11-02T21:05:57.510Z
gringer
<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>

CC BY-SA 4.0
2021-11-02T11:06:13.917Z
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?
juanjo75es
<assembly><busco>
BUSCO results apparently inconsistent
# 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?  

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## 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.


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