[GW_OK]

My Illumina sales rep told me:
Not sure how Illumina can enforce this, but the word is that it will.

Usage license. A piece of paper is signed saying you will only ever run Human WGS on these sequencers.

[williamhorne]

I bought the first two NextSeq 500's and basespace onsite. So if anyone has any questions please feel free to email me.

[M4TTN]

I bought the first two NextSeq 500's and basespace onsite. So if anyone has any questions please feel free to email me.

I'd be interested to know the costs of the various kits and the output you are getting (in cluster number).

[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.

[bilyl]

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.

Are you tied to Basespace for data management, or is there a way to copy to a networked drive (either as the run is being performed or after the run has finished)? I'd like to understand a little bit more about how the data is moved around.

[jwfoley]

Also what kind of connectivity does the thing have besides networking? Since it's targeted at mid-level labs and not large facilities, it won't always be in pipelines that immediately dump everything to a computing cluster, let alone BaseSpace. I just ran a month-old MiSeq yesterday that's not even networked (though we don't have gigabit ethernet so fat lot of good that would do anyway) and I had to copy out my data through a USB2.0 port - what year is this? So with NextSeq-scale data volumes, this matters.

[TonyBrooks]

Are you tied to Basespace for data management, or is there a way to copy to a networked drive (either as the run is being performed or after the run has finished)? I'd like to understand a little bit more about how the data is moved around.

You have the option of specifying a network location to mirror the run and send it up to BaseSpace for run monitoring. You can then use the new version of bcl2fastq to demultiplex and make fastq. There is no fastq only option for BaseSpace, you need to run it through a pipeline to make fastq and just ignore the results of the analysis.

[nucacidhunter]

With all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.

[AllSeq]

With all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.

You can do that, but the built in informatics will choke (it's expecting human DNA) and you'll be violating the agreement that the X Ten owner signed when they bought it. It probably won't take Illumina too much effort to figure out what's going on.

[jwfoley]

I think when you invest ten million dollars in machines that can only be used with consumables from one company, you don't take unnecessary risks that might be construed as a breach of contract.

[AllSeq]

With all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.

Now you don't need to! Illumina just opened up the HiSeq X to run non-human samples: http://www.businesswire.com/news/hom...e#.VhQNtdZPRuI

But it still only runs WGS. Any bets on when the application menu opens up?