Thinking about MiniON. Worth waiting to MkI B?

eicht021 · 05-16-2016, 02:03 AM

I'm keen to mess around with the MiniON to see where some long reads might play a role in future experiments of plant biodiversity. The early-access program sounds interesting, however would it be worth waiting a bit for the expected MkI revB? I'd imagine like most tech it will provide faster/longer/greater length outputs.

This is not a necessity for my research at the moment, more of something fun to get excited about.

So, jump in now or wait for rev B?

ECO · 05-16-2016, 10:10 AM

Can you do some simulations with the error rates and length distributions of the system?

Having spent some time in the single molecule sampleprep world, the challenge with obtaining "pure" plant gDNA will be a big hurdle...even more so in the PCR-based world of Illumina NGS.

eicht021 · 05-16-2016, 04:33 PM

I'm mainly interested in validating some short-read based transposable element variation (i.e. decent sized indels) across accessions. We are doing this at the moment with Illumina reads & split-read mapping and it would be interesting to see if we could get even some long reads spanning some of these non-reference insertions.

If error rates are still 15%+ it might cause some hassles. However I would hope with some fairly loose alignment parameters it would still be useful for its purpose.

I am concerned as well regarding sample prep. That would be part of the interest just to see if there is any useful data that could be gathered from using this platform rather than our standard Illumina suite. For the access program cost it should give me some idea while still costing less than a lane on the 2500.

Beyond my needs, I'm just curious if there are any expected big leaps from the MkI B compared to the initial MkI version. As this is more of a general curiosity on my part, I'd be happy to wait until the new & shiny version comes out. Are there any expectations as to what the MkI B would gain over the current version yet?

Ola · 05-17-2016, 02:25 AM

Quote:

Originally Posted by eicht021

I'm mainly interested in validating some short-read based transposable element variation (i.e. decent sized indels) across accessions. We are doing this at the moment with Illumina reads & split-read mapping and it would be interesting to see if we could get even some long reads spanning some of these non-reference insertions.

If error rates are still 15%+ it might cause some hassles. However I would hope with some fairly loose alignment parameters it would still be useful for its purpose.

I am concerned as well regarding sample prep. That would be part of the interest just to see if there is any useful data that could be gathered from using this platform rather than our standard Illumina suite. For the access program cost it should give me some idea while still costing less than a lane on the 2500.

Beyond my needs, I'm just curious if there are any expected big leaps from the MkI B compared to the initial MkI version. As this is more of a general curiosity on my part, I'd be happy to wait until the new & shiny version comes out. Are there any expectations as to what the MkI B would gain over the current version yet?

The big leap is with the new pore (R9) and base callers that are being released now. This chemistry also runs faster, at 250 b/s vs previous 70 b/s. Yield between flowcells is still an issue but accuracy with R9 should be much improved (2D accuracy up to ~95%). Mk 1B is a minor update that uses the same flowcells and will be free of charge for mk1 users. How much data and how long reads do you need?

wdecoster · 05-17-2016, 12:18 PM

Mk1B is a rather minor upgrade and will be available from next week. So most likely if you join the MAP now you will get a Mk1B (and if else, wait 2 more weeks

)

Ola · 05-18-2016, 03:09 AM

Just to be clear, the MinION early access program ended last summer. You can now register for access to the community and get a mk1 + start kit (2 flow cells + reagents) for $1000. Individual flowcells are then priced between $500 and $900 depending on how many you order.

gringer · 05-26-2016, 10:45 PM

Mk1b has an additional piece to shield the ASIC from fan noise, which is apparently a problem when sequencing at rates faster than about 500 bases per second. Clive Brown's goal is running at 1300 bases per second, which would be a theoretical maximum throughput of about 30Mb per minute, or 2 Gb per hour on the MinION. Clive has suggested that the MinION will be competing with the MiSeq on base quality and total read output in the not too distant future.

ymc · 05-30-2016, 06:24 PM

http://omicsomics.blogspot.hk/2016/0...-brownian.html

No more R7 now. This thread can now also go to the dustbin as well.

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05-16-2016, 02:03 AM	#1
eicht021 Junior Member Location: Australia Join Date: Oct 2011 Posts: 5	Thinking about MiniON. Worth waiting to MkI B? I'm keen to mess around with the MiniON to see where some long reads might play a role in future experiments of plant biodiversity. The early-access program sounds interesting, however would it be worth waiting a bit for the expected MkI revB? I'd imagine like most tech it will provide faster/longer/greater length outputs. This is not a necessity for my research at the moment, more of something fun to get excited about. So, jump in now or wait for rev B?

05-16-2016, 10:10 AM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Can you do some simulations with the error rates and length distributions of the system? Having spent some time in the single molecule sampleprep world, the challenge with obtaining "pure" plant gDNA will be a big hurdle...even more so in the PCR-based world of Illumina NGS.

05-16-2016, 04:33 PM	#3
eicht021 Junior Member Location: Australia Join Date: Oct 2011 Posts: 5	I'm mainly interested in validating some short-read based transposable element variation (i.e. decent sized indels) across accessions. We are doing this at the moment with Illumina reads & split-read mapping and it would be interesting to see if we could get even some long reads spanning some of these non-reference insertions. If error rates are still 15%+ it might cause some hassles. However I would hope with some fairly loose alignment parameters it would still be useful for its purpose. I am concerned as well regarding sample prep. That would be part of the interest just to see if there is any useful data that could be gathered from using this platform rather than our standard Illumina suite. For the access program cost it should give me some idea while still costing less than a lane on the 2500. Beyond my needs, I'm just curious if there are any expected big leaps from the MkI B compared to the initial MkI version. As this is more of a general curiosity on my part, I'd be happy to wait until the new & shiny version comes out. Are there any expectations as to what the MkI B would gain over the current version yet?

05-17-2016, 12:18 PM	#5
wdecoster Member Location: Antwerp, Belgium Join Date: Oct 2015 Posts: 97	Mk1B is a rather minor upgrade and will be available from next week. So most likely if you join the MAP now you will get a Mk1B (and if else, wait 2 more weeks )

05-18-2016, 03:09 AM	#6
Ola Member Location: Sweden Join Date: Aug 2011 Posts: 30	Just to be clear, the MinION early access program ended last summer. You can now register for access to the community and get a mk1 + start kit (2 flow cells + reagents) for $1000. Individual flowcells are then priced between $500 and $900 depending on how many you order.

05-26-2016, 10:45 PM	#7
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	Mk1b has an additional piece to shield the ASIC from fan noise, which is apparently a problem when sequencing at rates faster than about 500 bases per second. Clive Brown's goal is running at 1300 bases per second, which would be a theoretical maximum throughput of about 30Mb per minute, or 2 Gb per hour on the MinION. Clive has suggested that the MinION will be competing with the MiSeq on base quality and total read output in the not too distant future.

05-30-2016, 06:24 PM	#8
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	http://omicsomics.blogspot.hk/2016/0...-brownian.html No more R7 now. This thread can now also go to the dustbin as well.