Rapid Software Improvements
Looking at how Ion Torrent accuracy has improved over time. In this edition, I will show what a massive difference software can make with this technology. The results presented here was only possible because the software is open source. In addition, Mike and Mel have given me early access to binaries (ion-Analysis v1.61) that will be released in Torrent Suite v1.5.
There are three major areas that software can improve
- Throughput – Identify more Ion Sphere Particles (ISPs) with library fragments therefore increasing the total number of reads.
- Quality – More and longer reads aligning back to the reference sequence.
- Speed – Reduce the computational time to analyze the data.
The way I am going to present this data is to keep the data set the same (i.e. input DAT files) BUT perform the analysis using the different versions of the software, i.e. ion-Analysis. The ion-Analysis binary/software is responsible for ISP finding, signal processing and base calling. I have discussed signal processing and base calling in my previous blog posts. I have also briefly touched on bead finding ISPs but will go into more detail in my Signal Processing blog series. The three versions I have used are:
The table below shows that between versions 1.40 and 1.52 there was a modest increase in the number of ISPs identified (i.e. occupied wells), resulting in an increase in final library reads. There has been a slight decrease in version 1.61 which I will show in the next section it is quality and not quantity which is really important. Between versions 1.52 and 1.61 there is a massive difference in the filtering metrics. The blame has been shifted from Poor signal reads to Mixed/Clonal reads. This has massive consequence on how throughput can be increased further. The problem of poor signal reads is largely due to the quality of the raw data and the downstream computational processing, while mixed/clonal reads are due to sample preparation. There is a possibility that there is a bug in the pre-release code.