A first look at Illumina’s new NextSeq 500

[bryanbriney]

We're not doing any sort of analysis that involves alignment to a reference, but data quality from our PE150 NextSeq runs has been essentially identical to PE150 Rapid Runs on HiSeq.

[GenoMax]

Can someone here comment on the actual alignability/usability of the resulting data?

[bryanbriney]

We've had much the same experience as williamhorne. High Output produced roughly 500M reads, total output from a PE150 run was just shy of 150GB. We clustered at the high end of the recommended range, but still had about 80% Q30.

We've used the NextSeq with BaseSpace and it has some quirks. Run setup and sample entry is awkward if you have more than a handful of samples, although there's an option to upload an Excel file with sample info that we haven't tried yet. Never thought I'd say it, but the new run setup makes me miss Sample Sheets. On the other hand, once the run was going, BaseSpace works wonderfully.

As of right now, the NextSeq doesn't support dual indexes or custom indexes. Dual indexing is reportedly in the pipeline, not sure about custom indexes. Also, you can't start a run that exceeds the stated capacity of the reagent kit. MiSeq throws an error if you try, but it can be bypassed; NextSeq won't let you continue.

Overall, we're very happy. If read lengths get a little longer (come on, PE250!) and the BaseSpace quirks are fixed, the NextSeq will be darn close to perfect.

[williamhorne]

Using High output we are actually getting over 500 million reads per run. Unlike our GAII, and HighSeq, we actually have to pay very close attention to cluster density. The target cluster density for high quality samples is 1.75pM-2pM. Anything above and below will results in under/over clustering. So your samples need to be very exact with concentration.

These are solely made to be streamlined with the BaseSpace. Right now it only works with BaseSpace onsite, not in the cloud as they are having some majority broker issues that still are not resolved. Make sure you do your research in regards to output files and data in regards to basespace because it is not a visual machine. It gives you the output files and you must use 3rd party software on a different computer to view the results. Very annoying.

Overall very impressed with the NextSeq's, not so much BaseSapce.

[AllSeq]

We'd love to hear how it's working for you - actual outputs, how the data looks compared with previous Illumina machines. Basically anything you're willing to share! I'm sure lots of people are interested.

[williamhorne]

I bought the first two that were sold by Illumina including Basespace onsite. If interested in details let me know!

[AllSeq]

AllSeq was recently at Illumina HQ to get a sneak peek at their new NextSeq 500. We’ve already listed all of the specs and given our opinion on how we think this new platform fits into Illumina’s lineup and the broader market, but this was our first chance to see it in action. Check out our blog to see how it’s at once both tiny and huge.