New Challenges of Next-Gen Sequencing

I first started MassGenomics in the early days of next-gen sequencing, when Illumina was called “Solexa” and came in fragment-end, 35-bp reads. Even so, the unprecedented throughput of NGS and the nature of the sequencing technology brought a whole host of difficulties to overcome, notably:

• Bioinformatics algorithms developed for capillary-based sequencing didn’t scale.
• Sequencing reads were shorter and more error-prone.
• The instruments were expensive, limiting access to the technology
• Most of the genetics/genomics/clinical community had no experience with NGS
  

All of these are essentially solved problems: new bioinformatics tools and algorithms were developed, the reads became longer and more accurate, benchtop sequencers and sequencing-service-providers hit the market, and NGS was widely adopted by the research community. Mission accomplished!

Yet these victories were short-lived, because we find ourselves facing new challenges. Harder challenges. Here are a few of them.

1. Data storage

You’ve probably seen the plot of Moore’s Law compared to sequencing throughput. In short, the cost of DNA sequencing has plummeted much faster than the cost of disk storage and CPU. A run on the Illumina HiSeq2000 provides enough...