Busco result interpretation

Question

[popayekid55]

Dear all,

I have assembled a algal genome n predicted ~9k genes using Augustus. Genes were evaluated using Busco. Only 132 genes were put under different category of Busco (C,S,D,F and M). When I checked for C reinhardtii, around 300 genes were put under those categories. But in article they are telling ~80% (do not recall exact number) of d genes are complete.

My question is how to interpret Busco output??

Thank you

[lieven.sterck]

somewhat related issue :

A: Is BUSCO really better than CEGMA for genome assembly quality evaluation?

[lieven.sterck]

I recently was in a similar situation and in the end figured out that BUSCO is not really suited (adequate) for estimating completeness in algal genomes, mainly due to biases in their core gene set.

[popayekid55]

Any other approach you opted to address the concern??

[lieven.sterck]

Yes, the approach mentioned in that veeckman et al paper. Not sure if that is a public dataset though , they are colleagues from me here in the lab so I could easily get hold of it :)

Combined with more classical approaches such as fraction fo RNAseq mapped (and genes covered by etc) stats

Answer 1

[charles.bridges]

Not sure if CheckM will work for you, but I've found it extremely useful for bacterial genomes

[drikaul]

I think CheckM is primarily for bacterial and archaeal genomes

[bioinform_1]

Hi,

What is the best output for BUSCO? What does low number means? For example: C:18.4%[S:18.4%,D:0.0%],F:10.8%,M:70.8%,n:332

This is my Assembly stats:

Total length (>= 1000 bp) 1653501 contigs 8
Total length 1653501 Largest contig 1488929

Thanks

[lieven.sterck]

Hi bioinform_1,

just to mention it's not good practise to add new questions to an existing (old) thread. You're better off opening a new thread with your question.

I'll be happy to reply with advise/answers when you open a new thread ;)

thx.