In the coming days I will write and discuss the following major topics:
- Signal Normalization and Signal droop
- Correcting for incomplete extension and carry forward
- Bias and weakness in these current methods
This will be presented as a three part series, where I will provide my own code or pseudo code to demonstrate a point.
Before I start posting this series there are a few things I must write. I think Life Technologies has made a great move establishing the Ion Community allowing the free flow of information amongst members. Yes, some have criticize that it should be open like SEQAnswers but the difference is that within this forum a lot of intellectual property is discussed and exchanged and by having it closed and requiring registrations forces people to accept the terms and conditions. To join the TorrentDev part of the Ion Community, you do not need to own a PGM and besides this is the most interesting part of the Ion Community. The PGM Users section is just for people that like to beat their chest to show how great they are to others. I have benefited greatly from my interaction in the Ion Community, asking questions directly to people in R&D and getting an answer in less than 10 minutes in the morning. Yes, these people are bloody amazing! I will share a high level summary of what I have gained from discussing technical details with the active Life Tech contributors on the forum. I would like to thank Mike, Mel and especially Simon for their extremely detailed responses.
Secondly, it is great that Life Tech is willing to release the source code, that is making it open source to members of the Ion Community. Unfortunately, I will not be discussing any details of the code in this blog and these details are best discussed within the Ion Community. I will only discuss the high level concepts using my own code that does not rely on the code that was released. Looking at the approximately 20,000-50,000 lines of code and pulling it apart and summarizing the mathematics and modelling has been an excellent learning experience for me. It is quite rare, one has the opportunity to look at the nuts and bots of commercial software. I think the current members of the Ion Community should take the time to understand and learn from the code. I know they are not currently doing this as I seem to be the only one making them aware of things missing from the gzipped tarball that prevents the code from compiling. eg. the missing CUDA development libraries. Some may argue, why look at the code in the first place? And wouldn’t that influence any contributions you can make? My response is… firstly why reinvent the wheel? Secondly, it is good to know what methods have been attempted. The worse thing that could happen is that you attempt the same thing not knowing, but worse your attempt is quite lousy and inferior.
Lastly, the 1 million dollar accuracy challenge is a great idea to get the whole community involved and interested. I like to call it the “homopolymer problem”. Life Tech has taken a great approach with this, they are saying yes there is a bit to go to improve on these homopolymer errors but with the community’s help we can get there. Unlike Roche’s approach with the 454… “what homopolymer error, we don’t have any problems” and no you cannot see how we are currently dealing with it.
I believe the OPEN approach taken by Life Tech and the Ion Torrent being out there before the MiSeq makes it an easy target for unfair criticism. Most independent blogs and discussions online are quite negative or criticize Ion Torrent data and accuracy. Where is the faith that this technology will improve? I bet everyone was saying the personal computer was crap when it first came out and that everyone should be still running computers the size of your house! We got an Ion Torrent PGM because we saw the innovation and promise in the technology. Just remember this, No one can criticize the MiSeq because NO ONE currently owns one.
Anyways enough ranting, stay tuned for my three part series on the fundamentals of base calling.
Disclaimer: For the good of all mankind! This is purely my opinion and interpretations. I did not get paid by Life Tech to write this and am not under the influence of drugs while writing this.