Illumina versus Oxford Nanopore Technologies BUSCO Scores

Question

[Sarah]

Hello everyone, I was wondering if anyone has experience using Illumina and Oxford Nanopore Technologies to do a hybrid assembly of genomes? I have illumina and Oxford Nanopore reads and the BUSCO scores are vastly different to each other despite the sequencing being done with the same DNA extract. I wondered if anyone had a similar experience or could see an explanation as to why? Thanks!

[liorglic]

You mean you ran BUSCO on the reads? That doesn't make much sense, especially for short Illumina reads... Or do you mean you created two assemblies one using Illumina data only and one using ONT reads only? In this case, you should probably try a hybrid assembly approach as suggested. In general, the % of complete BUSCOs is usually positively correlated with the assembly size and N50, so if you improve these, you are likely to get better BUSCO results.

Answer 1

[colindaven]

Try a nanopore assembly with eg flye, and use the Illumina reads for polishing with eg hypo or racon. Medaka is also useful.

Illumina assemblies are highly fragmented which leads to poor busco scores. Please state the score you got out of interest, and the genome you sequenced, and the ONT chemistry.