Free NGS 1x50 SE rapid run

ianakiev · 07-14-2017, 10:31 AM

Hi All,

I have one Free Rapid 1x50 SE run to qualify my recently acquired HiSeq 2500. I thought it will be shame to waste it with PhX control, so I am open to hear your ideas and proposals for sequencing your library and why it will be interesting do so. It is absolutely free and there are no guarantees, however there is good chance to get some free data.

If you want to get in touch visit hera-bio (dot) com

Cheers,
Peter

Brian Bushnell · 07-14-2017, 10:44 AM

For qualification purposes, I think PhiX is a bit too simple, and a bad choice anyway because Illumina's calibration is PhiX-based. That said, human is also bad because it's diploid and highly variable which makes it harder to distinguish between variations and errors.

Though it's tempting to try to run an experiment during validation (and we do that all the time at JGI), I highly encourage you to resist the temptation! Rather, sequence multiplexed E.coli + something else completely different. Then you can calculate error rates, quality score accuracy, cross-contamination rates, insert-size distributions, GC and coverage-bias, and all the metrics you could ever want, without conflating factors that come from experiments.

ianakiev · 07-14-2017, 10:54 AM

Brian, thanks for your input. I will spike in some e-coli libraries that I already sequenced, however I still can fit in an experiment given the e.coli can be small fraction.
Thanks again.
Peter

huguesparri · 07-18-2017, 02:02 AM

You bought a HS2500? I thought the machine was being discontinued by Illumina.
Don't get me wrong: the machine itself is awesome, very flexible with high quality runs. We are using one for more than 3 years and are very happy with it.
It's just that the sequencing price is higher than what can offer a 3000 or 4000 (let's not talk about Novaseq). And as Illumina discontinued it (or at least, that's what our sale representative told us so), you might not expect new improvments on it.

Brian Bushnell · 07-18-2017, 01:03 PM

I'd still greatly prefer HS2500 over HS3000/4000... cost aside, it outperforms them in all my quality-related tests.

GenoMax · 07-19-2017, 04:20 AM

Quote:

Originally Posted by huguesparri

You bought a HS2500? I thought the machine was being discontinued by Illumina.

I don't think so. It is still prominently listed on Illumina's site. It is a workhorse and probably one of the best sequencers Illumina has ever made.

huguesparri · 07-19-2017, 04:42 AM

I agree with both of you regarding the quality of the machine itself. As I said, we have one for 3 years now and we are completely satisfied with it (set aside the price of the reagents).
But as previously said, our sale representative told us that Illumina was planning to discontinue it as well as Hiseq3000. Maybe she was wrong, or maybe Illumina did change their mind (or maybe they only plan to do it later...).

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07-14-2017, 10:31 AM	#1
ianakiev Junior Member Location: boston Join Date: Feb 2014 Posts: 9	Free NGS 1x50 SE rapid run Hi All, I have one Free Rapid 1x50 SE run to qualify my recently acquired HiSeq 2500. I thought it will be shame to waste it with PhX control, so I am open to hear your ideas and proposals for sequencing your library and why it will be interesting do so. It is absolutely free and there are no guarantees, however there is good chance to get some free data. If you want to get in touch visit hera-bio (dot) com Cheers, Peter

07-14-2017, 10:44 AM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	For qualification purposes, I think PhiX is a bit too simple, and a bad choice anyway because Illumina's calibration is PhiX-based. That said, human is also bad because it's diploid and highly variable which makes it harder to distinguish between variations and errors. Though it's tempting to try to run an experiment during validation (and we do that all the time at JGI), I highly encourage you to resist the temptation! Rather, sequence multiplexed E.coli + something else completely different. Then you can calculate error rates, quality score accuracy, cross-contamination rates, insert-size distributions, GC and coverage-bias, and all the metrics you could ever want, without conflating factors that come from experiments.

07-14-2017, 10:54 AM	#3
ianakiev Junior Member Location: boston Join Date: Feb 2014 Posts: 9	Brian, thanks for your input. I will spike in some e-coli libraries that I already sequenced, however I still can fit in an experiment given the e.coli can be small fraction. Thanks again. Peter

07-18-2017, 02:02 AM	#4
huguesparri Member Location: Montpellier (France) Join Date: May 2008 Posts: 93	You bought a HS2500? I thought the machine was being discontinued by Illumina. Don't get me wrong: the machine itself is awesome, very flexible with high quality runs. We are using one for more than 3 years and are very happy with it. It's just that the sequencing price is higher than what can offer a 3000 or 4000 (let's not talk about Novaseq). And as Illumina discontinued it (or at least, that's what our sale representative told us so), you might not expect new improvments on it.

07-18-2017, 01:03 PM	#5
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	I'd still greatly prefer HS2500 over HS3000/4000... cost aside, it outperforms them in all my quality-related tests.

07-19-2017, 04:42 AM	#7
huguesparri Member Location: Montpellier (France) Join Date: May 2008 Posts: 93	I agree with both of you regarding the quality of the machine itself. As I said, we have one for 3 years now and we are completely satisfied with it (set aside the price of the reagents). But as previously said, our sale representative told us that Illumina was planning to discontinue it as well as Hiseq3000. Maybe she was wrong, or maybe Illumina did change their mind (or maybe they only plan to do it later...).