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Old 05-13-2014, 12:36 PM   #5
Junior Member
Location: San Diego

Join Date: May 2014
Posts: 8

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.

Last edited by bryanbriney; 05-13-2014 at 12:40 PM.
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