Supposedly, if you need long reads of high quality and throughput, you should be using GS FLX+, yielding 750-800 peak read length, from Roche/454, right? Illumina reads are getting longer, but 250 is for now the limit (notwithstanding the 300 bp run done by the broad). IonTorrent promises 400 bases, but we will have to see what the quality is going to be. And PacBio, well we all know they are long, but with relatively low throughut and quality peaking at 85% – 86% accuracy (useful nonetheless).
Commercially, GS FX+ had been around for more than half a year. So far, the community is reporting some success, see this thread at SeqAnswers. But, there are problems all around when you talk to people. Our own centre (the Norwegian Sequencing Centre) got the upgrade in August. I’ll spare you the details on numerous control/test fragment runs, short read runs etc, but the bottom line is that we still haven’t been able to sucessfully sequence a FLX+ library on our GS FLX+. Right now, we are having a service visit, and I intend to chain the guy to the instrument until we see some real good data from one of our own libraries…
There is another thing that surprises me too: I am attending PAGXX, the Plant and Animal Genome conference in San Diego, where Roche is one of the main sponsors. However, when you look at the little text they have as an exhibitor, well, let me just quote a part of it for you (source): Continue reading →