DNBseq vs Illumina

Question

[ev97]

We are thinking to do RNA-seq and while we were asking for budgets from different companies... we have received an offer to use DNBseq platform.

Does anybody have worked with this tecnology? We are used to work with Illumina and although we have searched different opinions (no success), we do not know anybody who has worked with it to ask.

Any help will be really appreciated.

Thanks in advance!

Answer 1

[GenoMax]

DNBseq has been around for some time and was mainly used in EU and asia because of patent litigation. That has been resolved and now the sequencers are available world-wide.

There should not be much difference in the results. Here is a recent comparison: https://pubmed.ncbi.nlm.nih.gov/33864614/

That said, if you have prior data done on Illumina you may want to stay on the same platform to avoid having to add a batch control variable for that particular set of data.

[ev97]

Thanks very much for the feedback! I haven't thought in the last point that you mentioned if I want to compare with previous data and definitely it is a good point to think about it before making any decision. Thanks very much!

Answer 2

[Zhenyu Zhang]

Pros

• cheap
• they do all kind of variant calling for you (if you don't know how to do that, or lazy)

Cons

• the quality was not good 10 years ago. I know since they were brought by a Chinese company, the quality improved, but I don't know how much
• different from other illumina data

[colindaven]

Quality is fine these days - well, the last data I had was about 2 years ago. The sequencing world was a very different place 10 years ago! Was fine for variant calling, actually better compared to the Illumina Nextseq550 , so should be more than OK for RNA-seq.

[ev97]

Thanks to you both! I really appreciate it. colindaven @ZhenyuZhang