TANGENT!: Comparison Charts for NGS Platforms 2013

If you are thinking about buying an NGS platform...

Travis Glenn has released the 2013 tables comparing NGS platforms seven ways from Sunday, so you can make an informed decision.

I found them on a blog I follow: www.molecularecologist.com

Table 1a-c: de novo, resequencing and other applications. NGS Platform grades.

Table 2a: Runtime, reads and yield

Table 2b: Costs/run, Costs/MB, minimum costs

Table 3a: Instrument Costs

Table 3b: Computation Resources

Table 3c: Error Rates

Table 4: Advantages and disadvantages of each instrument

Citation: Glenn, TC. 2011. Field Guide to Next Generation DNA Sequencers. Molecular Ecology Resources. doi: 10.1111/j.1755-0998.2011.03024.x

Blog Series: WoG, Cesky Krumlov; Day 1: Amazon Cloud

The Amazon Cloud
Dr. Konrad Paszkiewicz
Director, Wellcome Trust Biomedical Bioinformatics Hub

Topic: Amazon Cloud

Pros

• No need to house/maintain servers
• No need to worry about backing up
• Only pay for what you use
• Upgrade are handled by Amazon
• You can expand and delete storage as you have need
• There are many many preconfigured virtual machines (VM) to pick from if you don't want to develop one on your own (QIIME, STACKS and Short read aligment all have their own VMs)

Cons

• You will pay for it; storage even when you are not using it, time using it etc and many researchers are resistant to the idea that they have to 'pay' for computing power and storage. And they are surprised by how much computational power and storage can cost. Researchers need to start being trained to think of about computing costs in their grant proposals--cost of programming and software, costs of hardware, costs of the people that will need to be hired to program and do analysis.
• Cost of an Amazon VM can run 0.20-3.00/hr; you also pay by the Gigabyte.
• Data transfer to your VM could be slow
• If the network is down you won't be able to access your VM
• Typical per month cost is $200-$400 depending on how much data you store and how extensively you use the machine. So you have to decide is it worth it? What are the costs and benefits of buying and maintaining your own server or computing system that's powerful enough to run analysis and store all your data versus using Amazon web services.

Read on if you are interested in the tutorial/exercise we went through today despite it most likely not being applicable to your situation unless you have access and/or are interested in implementing amazon cloud services.