BUSCO, Gene duplication

Question

[lukhanyomakhabane]

Hello everyone

What tool can someone use to analyze for gene duplication for fungal genome of interest. I have used BUSCO to evaluate genome completeness of my genome interest. BUSCO output files also include Complete and duplicated BUSCOs. Is it a wise to conclude on gene duplication for a genome based on duplicated BUSCOs? Your help would be greatly appreciated, thanks in advance!

Answer 1

[Buffo]

No, is not, from BUSCO's description:

Using datasets of near universal single-copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content.

To calculate gene duplication you should use different tools, MCL is probably one of the most popular algorithms for such tasks.