Increasing Productivity in NGS Research
Blog Oct 31, 2013
BioDatomics introduced the company’s first commercial product at the American Society of Human Genetics (ASHG) 2013 meeting in Boston. BioDT™ is an open source suite of next generation sequencing data analysis software and services aimed at addressing the shortcomings found with current data analysis offerings by delivering much higher performance and an intuitive interface
We spoke with BioDatomics' Co-Founder and Chief Marketing Officer, Alan Taffel to learn more about data analysis in NGS and how BioDT enables quicker analysis.
AB: How much of a bottleneck is data analysis in NGS?
Alan Taffel (AT): Data analysis is THE bottleneck in NGS. Modern sequencers are very efficient at sampling genomes and delivering the associated data as FastQ or BAM files. Analyzing that data takes time for three reasons: 1) researchers or bioinformaticians must program a “workflow” that will perform the desired analysis on the data; 2) the workflow must be executed, which can take days or weeks; 3) the tabular results must then be further analyzed to gain actual insights.
AB: What problems do users face when analysing big data?
AT: Quite a few. Specialized skills are required to create workflows and to analyze the results of their execution, which means bioinformaticians must get involved, and they can be a scarce resource. Also, researchers could be much more efficient if they could collaborate with each other in real time, but current analysis platforms, other than BioDT, do not have such a capability. Finally, since most analysis platforms are closed source, researchers are restricted to a limited set of proprietary workflows.
AB: How does BioDT enable quicker analysis?
AT: Aside from allowing researchers and bioinformaticians to create and modify workflows with a simple drag-and-drop interface, and then visualizing results rather than presenting them as inscrutable tables, BioDT executes workflows up to 100x faster than other platforms. This is achieved by means of a specialized execution engine, which breaks workflows up into parallel tasks rather than one long serial task, combined with the Big Data analysis capabilities of Hadoop.
AB: What does quicker data analysis enable?
AT: Workflows that currently take days or weeks on other platforms can be executed in just hours on BioDT.
AB: How has BioDT been received so far in the market and how was it received at ASHG?
AT: Most visitors to the BioDatomics booth at ASHG were initially skeptical that BioDT represented a true advance in research productivity. It is safe to say that none left unconvinced. This impression is born out in the market. Digicon, an IT services provider to the U.S. government (especially NIH) canvassed the market for a bioinformatics analysis platform, and after rigorous evaluation chose BioDT. Similarly, the prestigious J. Craig Venter Institute, which is intimately familiar with all bioinformatics platforms, has gone on record (see press release) with accolades for BioDT.