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
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popayekid55
1 answer
Not sure if CheckM will work for you, but I've found it extremely useful for bacterial genomes
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
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.
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somewhat related issue :
A: Is BUSCO really better than CEGMA for genome assembly quality evaluation?
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.
Any other approach you opted to address the concern??
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