I'm not a bench scientist (have not done lab work in well over a decade), but one thing I caution you to consider in costs is that of analyzing the data. Depending on just what your project is and how big it is, expecting to complete data analysis on a simple off-the-shelf desktop or even a basic server may be unrealistic. Many of us use, and need, large memory machines, mulcti-core servers or clusters (at least a small cluster) to handle next-gen sequence analyses.

Luckily, almost all of the software you may need is likely available free as open source tools. The catch to that is that often it is only for UNIX/Linux and is also often command line only, so if need be, you may have to learn some basic command line UNIX.

I just mention all this because all too often I have seen people sink much time, money and effort into generating next-gen data, only to be brought to a slamming halt when they realize they need new computing hardware, or money for analytical services, to do anything with it.

Sequencing has gotten much cheaper. Runs typically cost $1,800-$3,000 (could be cheaper), but expected to drop down to $1,000 for the end of the year. The biggest cost, however, would be the reagents needed to sequence. That's the current bottleneck. You're probably looking at $25K for the reagents needed per run. There's also Illumina, ["sequencing by synthesis"], so you should take a look at their method too. One thing you have to think about is if the soil sample has homopolymer repeats, and such, because IonTorrent doesn't handle them well yet. Know the weaknesses of all the machines before making a choice.

Hope this helps, and please ask more questions if you need more info.

Cheers,

JR

the platform you choose depends on how much output you want/need. for broader metagenomics, 454 is becoming obselete - only giving about 400 MB data per run - illumina on the other hand is giving 30 GB per run at about 1/5 the cost. maybe details of your intended project for sequencing would help.

also, aside from the actual sequencing costs....library preparation can be quite expensive. if you have a lot of samples the library prep may cost more than the sequencing.

we do about 12 samples per illumina lane (30 GB of data) and that generally runs us about $3000.

I'm not a bench scientist (have not done lab work in well over a decade), but one thing I caution you to consider in costs is that of analyzing the data. Depending on just what your project is and how big it is, expecting to complete data analysis on a simple off-the-shelf desktop or even a basic server may be unrealistic. Many of us use, and need, large memory machines, mulcti-core servers or clusters (at least a small cluster) to handle next-gen sequence analyses.

Luckily, almost all of the software you may need is likely available free as open source tools. The catch to that is that often it is only for UNIX/Linux and is also often command line only, so if need be, you may have to learn some basic command line UNIX.

I just mention all this because all too often I have seen people sink much time, money and effort into generating next-gen data, only to be brought to a slamming halt when they realize they need new computing hardware, or money for analytical services, to do anything with it.

That is true, I always warn my collaborators about this...many dont understand the volumes of data they will be getting. If you cant find a collaborator there are services available for fee.

Michael Black is absolutely right. I'd like to re-emphasize that you want to focus on an architecture that has LARGE memory. Don't leave out that detail. It's one thing that you'd need to look for when you're looking at different services.

Carlos, could you list out which free services you're referring to that would be adequate for NGS? Thanks!

I'm afraid Carlos said "for fee" and not "for free"... But if there are any services for free I would be glad to hear about them too XD

Yeah, me too

Thing is Its tough to make any comment . Both of the platform has issues... One thing you may find interesting is, Ion torrent would be cheaper, if your sample size is small but genome size, more or less larger... But if you have small target region, with large sample number, 454 would be cheaper option. Again, read length of 454 always greater than ion torrent. It would increase you map ability. But theior, base calling algo has some issues. Ion's base calling is comparatively better (according to my experience). 454 has excellent assembler " Newblar" ...so and so...

For the data analysis maybe, but if you need to do the assembly yourself from the raw data, a common workstation (although being better than a desktop computer or a laptop) is clearly not enough.

Anyway, if you have no previous experience on computational biology and you are not really interested in spending too much time learning its ins and outs it will be better for you to find an experienced collaborator or contract the sequencing together with the data processing.

Yusuf Khan - I only mentioned analysis cost since I have no idea what the scope or size of the project under consideration will be or at what point the investigator(s) will be picking up the analyses. If all they are thinking of doing is paying to get raw sequence reads, then an off-the-shelf desktop machine is going to be limiting (to say the least).

If they will be paying to receive data ready for tertiary analysis, they may be alright with whatever computing resources they currently have (or have access to), but even then, they need to keep in mind that many commercial centers consider primary/secondary analysis as an additional charge on top of actual library preparation and sequencing.

We do our sequencing in-house (ABI SOLiD 5500xl - so far mostly Rat whole transcriptome data) so I handle data directly from the sequencer to final published results, and I could not do that if all I had was my basic Dell desktop machine.

Whether they are paying a company or core facility for it, or doing it in-house, analysis needs to be factored into costs of any project. Just my opinion, but I have seen many who have failed to think about that beforehand and end up frustrated when it comes time to finish a project and there is no money left in the budget to finance whatever data steps are left to be completed.

Hi Yusuf, our lab also decide to use Illumina workflow to make a NGS, to find out the mutations among patients. I wonder the detail about cost what you said. For instance, the aim is very simple, to find out the mutations, whether our have to learn how to deal with the huge data of NGS, and find out the mutations by ourselves? rather than done by Illumina already? If it is true (analysis the mutation by ourselves), we have to spend much more money, time and labor on such work, then the NGS seems isn't a good deal. After all, we can not ask our Posdoc familiar with computer or UNIX.

Hello Silvia,

This is perhaps a bit late in the game, but just in case...

One of our lab's bioinformaticians shared this spreadsheet with me many years ago (around 2009? I think...) when we were starting on large scale sequencing. It is always kept up to date and has always been a good reference on the different sequencing technologies available.

https://docs.google.com/spreadsheet/ccc?key=0AvaxS3m5rl-9dHdtUGRtaGlsZWNFNWJleDRXaUhQTHc#gid=0

Best,

Chris

PS: Please let me know if you can see the spreadsheet or not, I tried on firefox and chrome, not logged in on google, and it worked...)

Hi Chris,

Every answer is really helpful. I can see the spreadsheet. Thanks for the link!

Hi Silvia

We are finding Ion Torrent easy to use for soil.

See Whiteley, A.S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullen, B., Allcock, R., O’Donnell, A., Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform, J. Microbiol. Methods (2012) for the protocol

Regards Dan

Hi there,

I am a very happy user of MiSeq by Illumina. A great sequencer for small genomes.

See the link attached for price comparison of different platforms.

Hope that helps. Good luck!

http://nextgenseek.com/2012/08/comparing-price-and-tech-specs-of-illumina-miseq-ion-torrent-pgm-454-gs-junior-and-pacbio-rs/