Low BUSCO output

Question

[bioinform_1]

Hi,

What is the best output for BUSCO? What does low number means?

Busco stats:

C:18.4%[S:18.4%,D:0.0%],F:10.8%,M:70.8%,n:332

Assembly stats:

Total length (>= 1000 bp) 1653501

contigs 8

Total length 1653501

Largest contig 1488929

Blast with reference:

Query coverage - 95% Per. Identity - 99.4%

Why is the BUSO number so low with high similarity with Reference?

Reference BUSCO: C:94.3%[S:94.3%,D:0.0%],F:0.6%,M:5.1%,n:332

Thanks

Answer 1

[Mensur Dlakic]

It is difficult to answer this question without knowing the expected genome size and the type of organism. Also, what is the phylogenetic group used for comparison (your reference)?

Generally speaking, you seem to have an excellent assembly if this is a prokaryotic genome. Although I don't use BUSCO directly, others around me who do indicated that it may be too stringent in assessing completeness. I have seen somewhat puzzling BUSCO analyses similar to yours for what seem to be fairly complete eukaryotic genomes. Don't have enough observations to generalize, but it fits with experiences of others.

If this is for a prokaryotic genome, I recommend CheckM as my impression is that it is more widely used in the literature.

[bioinform_1]

Hi Mensur Dlakic,

Thank you for the information.

These are prokaryotic bacteria. The reference and the assembled bacteria are same species (same phylogenetic group). The expected genome size is ~1.7mb. My strain was sequenced with MinIon.

I will try CheckM and see how it looks.

Thanks