Sure Select on Illumina....

[VanessaS]

I just had a little chat with the sales rep for Illumina and he was telling me some pretty fantastic things about the HiSeq, with regards to exon capture and sample throughput. I'd like to know what those of you who are using either the GAII or the HiSeq are actually getting in the field.
He tells me that you should get 200 GB/flowcell or 400gb per run, 8.3Gb per sample so roughly 140x coverage, when putting 3 samples per lane, for the HiSeq. So thats 24 samples per flowcell, 48 per run. All getting 140x coverage. I have not checked his math, just parroting.

How accurate is this? We have the solid 4's and were doing 1 sample per quad, which is 4 samples per flowcell and 8 per run, and getting something like 30 x coverage, I think. We are switching to the multiplexing protocol, and will be doing 4 samples per run, to try and increase coverage. We will be using the 50MB human all exon sure select kit.

If what the sales rep is saying is true, that I can get 48 samples on the illumina and only 4 on the solid, Illumina starts to look pretty darn attractive for this particular application!
So what do you folks do? How many samples do you put per lane, per run and what kind of coverage do you get?

Thanks for any elucidation!

[Jessica_L]

Hi Vanessa--

Our absolute lowest numbers off the HiSeq tend to be about 40-45Gb per flowcell (occasional library prep problems, or maybe just a shorter run). I think the max we've been able to pull off so far has been more like 100Gb per flowcell, an average of about 60 to 65Gb. The instrument definitely has the capacity to go higher-- we're usually burning one channel for a dedicated PhiX control lane because of some QA/QC issues that have been happening with flowcell lots from Illumina. That problem appears to have been solved, but we're sticking with the control lanes for now.

Also, we've not completely moved over to the TruSeq reagents which *are* supposed to improve yields and data quality. What you're being told about 150-200Gb for a 2x100 PE read may not actually be far off. Additionally, Illumina has been publicizing a new version of the TruSeq reagents and some software upgrades that will take the yield up to 600Gb. I assume that's for two flowcells, but I'm not sure.

Hope that helps.
Regards,
Jessica