[Jeremy]

Any updates on the MiSeq vs Ion comparison?

[pmiguel]

http://www.forbes.com/sites/matthewh...marketing-war/

Thanks for the link.

I think the MiSeq as a platform currently beats the Ion Torrent. But there are issues at work here that are not considered in the Forbes article.

Illumina (Solexa) took and early lead over Applied Biosystems in the next generation sequencing realm from the start and never allowed that lead to diminish. There were various factors in play, but most tellingly was the agility with which Illumina developed and deployed new technologies.

However, with Life Technology's acquisition of Ion Torrent, it seems to me that factor -- the raw drive and ability to advance for this instrument system is at least on par with that of Illumina.

Face it, when you buy a sequencer today, you are purchasing not just what it is now, but what it will become via hardware retrofitting and new chemistry over the coming months and years.

This is a front upon which I do not think Illumina has been attacked before. Previously they were the rapid innovators against the lumbering Life Technologies (SOLiD) and Roche (GS-FLX) behemoths. Alas, I am seeing some signs of weakness in Illumina's capabilities in this regard:

(1) The v2 chemistry roll-out for the MiSeq has been slower than expected, and disjointed. Currently the Illumina website will extoll the virtues of v2 and, as of today, even advertises the reagents for sale. But the MiSeq Control Software 2.0 necessary to run the new chemistry remains unavailable.

(2) Detailed information necessary to utilize the MiSeq as an amplicon sequencing platform -- an absolute requirement for a 454-replacement and, indeed, to compete with the the Ion Torrent -- is still difficult to come by. Maddeningly, the underlying components to accomplish this are readily available. It harkens back to Roche's insanely long delay in releasing an official cDNA sequencing methodology.

(3) Illumina is succumbing to the allure of the "intellectual propertization of methodology". Instead of deliberately open sourcing all their recommended library construction technologies, they are becoming increasing furtive about releasing information to their own customers. Their refusal to detail the sequence and concentrations of many of the primers included in their SBS and clustering kits is an outrage and an impediment to their customer's ability to pick up the amplicon "baton" that they have dropped.

All of the above are indications to me of a "hardening of the arteries" of Illumina. While they have achieved dominance for the time being, I think they would do well to contemplate how they came to this juncture and realize they are vulnerable to attack from the same flank they have used to fell the previous giants in this arena.

--
Phillip

[ningwang]

I think pmiguel makes an important point here

When you're buying a machine, you're not just buying for the capabilities today, but how it's going to develop in the future. I suspect both companies will be able to improve on raw accuracy and Gb/run, but there are inherent "issues" with both technologies to consider. What I'd be interested in knowing are:

1. Ion Proton's chemistry has a well-known issue calling homopolymers. I've always wondered why they don't have a second option that uses modified nucleotides so users can decide for themselves whether or not they want to trade higher accuracy for a longer run time. In any case, I hear recent software upgrades have improved Ion's homopolymer issue, but I wonder how much more they can do here.

2. Ion Proton will likely have a huge advantage if you measure throughput by time (as opposed to per run). Imagine once you get to 250Gb per run (which Ion claims P3 will be in less than 2 years), do you really need higher throughput per run unless you have a need for some serious multiplexing? I suspect by then, your throughput advantage would only come in reducing the run time. What else can Illumina do to reduce Miseq's run time, or are they fundamentally restricted by the chemistry & camera speed? If Illumina needs to change either one, your existing Miseq would probably need a major upgrade/replacement to keep up.

[krobison]

2. Ion Proton will likely have a huge advantage if you measure throughput by time (as opposed to per run). Imagine once you get to 250Gb per run (which Ion claims P3 will be in less than 2 years), do you really need higher throughput per run unless you have a need for some serious multiplexing?

For metagenomics, it's hard to imagine ever deciding you have enough throughput :-)

Also, if you are sequencing some plant genomes, you would find this useful -- members of the lily family often have genomes 50X the size of human (!)

[james hadfield]

Ahhrg! The image on slide number 11 for the 2500 flowcell comes from my blog. It was a mock up from a decscription and there is now a real flowcell to look at.

[mattarno]

so it only has two lanes? is that because of higher depth per indexed sample?

[cement_head]

Hi All,

Great thread, very helpful. We are also seriously looking at both the ION Torrent PGM and the MiSeq systems. We can only afford one - but there's a twist to our situation. I run a core DNA/Genomics lab and we are an "open" lab - that is, we train users on the instrumentation and they do the actually wet work themselves (a few exceptions). So, in this case, it looks as though the MiSeq would be far and away the best choice.

However, we have several universities within about twenty minutes that have both MiSeqs and HiSeqs avaiilable. So, people who are interested in de novo, or in RNASeq are more likely to use the MiSeq to test the library for a HiSeq run. So, it might be better to have a different instrument available at our facility, and it seems that targeted amplicon sequencing is much better and easier on the ION Torrent.

It's really difficult to choose because, as has been pointed out, one is really buying into the "future" of these machines, and no-one wants to get stuck with a lemon/lemon-tech. I'm starting to lean towards the MiSeq, because of it's ease-of-use.

Has anyone that has recently purchased an ION Torrent care to share thier experiences?

Still undecided,
CH

[Gorbenzer]

Hi All,

Great thread, very helpful. We are also seriously looking at both the ION Torrent PGM and the MiSeq systems. We can only afford one - but there's a twist to our situation. I run a core DNA/Genomics lab and we are an "open" lab - that is, we train users on the instrumentation and they do the actually wet work themselves (a few exceptions). So, in this case, it looks as though the MiSeq would be far and away the best choice.

However, we have several universities within about twenty minutes that have both MiSeqs and HiSeqs avaiilable. So, people who are interested in de novo, or in RNASeq are more likely to use the MiSeq to test the library for a HiSeq run. So, it might be better to have a different instrument available at our facility, and it seems that targeted amplicon sequencing is much better and easier on the ION Torrent.

It's really difficult to choose because, as has been pointed out, one is really buying into the "future" of these machines, and no-one wants to get stuck with a lemon/lemon-tech. I'm starting to lean towards the MiSeq, because of it's ease-of-use.

Has anyone that has recently purchased an ION Torrent care to share thier experiences?

Still undecided,
CH

Hi,
i can suggest you (if you can) to wait for some One Touch 2 feedbacks and feedbacks about the 400bp kit that will be releasing soon...

[cement_head]

Well, Illumina is offering a pretty good trade-in on old ABI CE Genetic Analyzers against a new MiSeq ($26,000 USD).

[pmiguel]

Well, Illumina is offering a pretty good trade-in on old ABI CE Genetic Analyzers against a new MiSeq ($26,000 USD).

You can get a much better price for a 3730XL than $26K from a scientific instrument reseller. Might be a good deal for other platforms though.

[cement_head]

That's for 310!

[Buzz0r]

New skin for PGM? Did they only change the skin or did they also change some technical details of the PGM?

Are they trying to confuse you with the PGM and Proton skins now as they confuse you on the talks with data from PGM and Proton (which they dont show!) ??

[DNA Sorcerer]

Just the skin, and hid the hoses and secured the reagent bottles.

[jdelton]

We have two PGM and a Proton. I really like the machines. However, a lot of what I like about them is the fact they are not mature yet and have a lot of space to grow. I think just like 454 (we have two of those as well) was dominate for a long time, then reached its plateau and was overcome, I believe MiSeq (we work with another lab that owns a MiSeq even though we don't own one ourselves) is right at that junction too. They won't be able to extend their length very much further (in my opinion) and they won't have much more room to extend capacity. However, PGM is at an easy 400 bp (we had an amplicon run closer to 500 with no change in the number of flows). Getting over the specs on the chips is easy to do as well with the V2 chemistry and chips. For the Proton, the size is right at 200bp fragments, and there every indication it will jump to the 400bp size of the PGM at about the same speed the PGM did. In addition with the new Avalanche technology that eliminates the emPCR step (and supposedly is giving 600bp reads in house) as well as the Chef machine to take care of the post-library/pre-sequencing steps and bigger chips (250gb at spec and all of the other chips perform easily over spec with longer reads i.e. 100+mb on a 314 chip, 400-500mb on a 316 chip) there is no reason to expect that the Proton will have any problems surpassing miseq very quickly.

[pmiguel]

We have two PGM and a Proton. I really like the machines. However, a lot of what I like about them is the fact they are not mature yet and have a lot of space to grow. I think just like 454 (we have two of those as well) was dominate for a long time, then reached its plateau and was overcome, I believe MiSeq (we work with another lab that owns a MiSeq even though we don't own one ourselves) is right at that junction too. They won't be able to extend their length very much further (in my opinion) and they won't have much more room to extend capacity. However, PGM is at an easy 400 bp (we had an amplicon run closer to 500 with no change in the number of flows). Getting over the specs on the chips is easy to do as well with the V2 chemistry and chips. For the Proton, the size is right at 200bp fragments, and there every indication it will jump to the 400bp size of the PGM at about the same speed the PGM did. In addition with the new Avalanche technology that eliminates the emPCR step (and supposedly is giving 600bp reads in house) as well as the Chef machine to take care of the post-library/pre-sequencing steps and bigger chips (250gb at spec and all of the other chips perform easily over spec with longer reads i.e. 100+mb on a 314 chip, 400-500mb on a 316 chip) there is no reason to expect that the Proton will have any problems surpassing miseq very quickly.

The miseq is Illumina's bench top instrument. I thought the Proton was to compete with the HiSeq, not the MiSeq.

Actually as of 4th quarter last year the Proton was trumpeting its coming supremacy quite vigorously. I attribute this as the cause of Illumina's early release of 2500 upgrades.

But since last year, I have heard nothing about the Proton. You say you are getting 250gb/chip? Is that 200 bases a paired end read (2x200?)

--
Phillip