Hello, I used BUSCO to assess the quality of a de novo green algae genome assembly and I received this result: C: 94.3%[S:19.8%, D:74.5%], F:1.8%, M:3.9%,n:1519 C:1433 [S:301, D:1132], F:28, M:58, n:1519
I am wondering what a normal level of duplication would be to expect for a plant/algal genome and reasonings why this might be so high for mine?
Should I be considering removing some of this duplication? How can I detect where it is and how can I remove it?
My genome is larger than expected so that is why I am concerned about the duplication level. Any advice is appreciated. Thank you!
•
written
by
brooklyn •
1 answer
It is normal to have some gene duplication, but I would not expect 75%. It could mean several things:
- polyploidy
- contamination with a related genome
- artificial contamination due to sequencing errors stemming from very deep sequencing
How identical are your duplicated regions at nucleotide and protein levels? That may help answer why they are there in the first place.
Log in to answer this question.
-
Low busco scores after annotating genome using same model as another species in genus
written by Wilber0x •
-
What does the 'E%' represent in BUSCO results?
written by 林明德 •
-
What does heterozygosity mean in a haploid genome?
written by brooklyn •
-
High duplicate BUSCOs after annotation but not assembly
written by jaredbernard •
-
LOW BUSCO Score for De novo genome assembly
written by siu
-
When a duplicated BUSCOs value is too high? Reasons and how to improve it
written by resug •
-
assembly without trimming vs with trimming
written by tiagobellintani •
-
Low BUSCO output
written by bioinform_1 •
-
Choosing a de novo assembly for DGE analysis
written by User 4014 •
-
Busco result interpretation
written by popayekid55
