In order to evaluate Illumina Complete Long Reads (CLR), I thought it might be interesting to compare them to PacBio Continuous Long Reads (CLR)1. So, in this post let’s think through some of the differences between CLR and CLR.
The performance characteristics of CLR and CLR differ in some respects. The reads generated by CLR naturally have a relatively high error rate. However, because these errors are largely non-systematic a CLR consensus can correct for these errors (a similar process exists in CLR). Of course company statements suggest that CLR is “not a synthetic long read technology”. This is debatable, but in contrast to this CLR clearly is a “single molecule level” technology. In my opinion this gives CLR a slight edge over CLR.
In the case of CLR, reads can benefit from correction using non-CLR reads from the vendors short read platform. Similarly CLR reads could also benefit from correction using non-CLR reads from the vendors short read platform. Or vice-versa! There’s nothing to stop you doing it the other way round! But there are likely cost advantages to going with the CLR vendors short read platform (this would also be true in CLRs case).
A full systematic evaluation of CLR over CLR would be interesting, particularly if assembling the longest “not synthetic” read is your goal. My guess is that CLR might have a slight edge over CLR here.
To be honest I don’t get the impression that CLR has played well in the market so far (this is of course true for CLR).
Overall I’d suggest that other technologies such as PacBio Hifi reads (where you need high accuracy) or ONT reads (where lower accuracy is acceptable, but you need the longest reads possible). Might be a better fit for most applications.
In any case I will keep watching for development in CLR (and CLR). CLR always seemed like a neat approach but perhaps one limited to niche applications. But, I hope we get to revisit CLR (and CLR) at some point and see developments based on these approaches.
Readers should note that this post is not entirely serious…