SNPGenie Software Goes Online

SNPGenie, my new software for pooled next-generation sequencing analysis, is now available at GITHUB. It recently won the F1000 Poster Prize at the Great Lakes Bioinformatics Conference (International Society for Computational Biology), and represents a major direction for my doctoral research.

What does it mean for sequencing to be “pooled”? When one thinks of DNA sequencing, one usually imagines the DNA of a single individual being decoded into its A’s, C’s, G’s, and T’s. However, given advances in biotechnology, it is now possible to sequence pools of genetic material containing DNA (or RNA) from multiple individuals. For our purposes, this has been especially useful for analyzing the multiple viral genomes present in a blood sample of an infected host, like the H5N1 influenza virus infecting a ferret. When you do this, you get to see what kinds of genetic variants are floating around in the population of interest, and what statistical patterns emerge. The result is a better understanding of how viruses change while infecting a single host (within-host evolution) and when transmitting to a new host (between-host evolution). Clinically, this approach may ultimately allow a better understanding of how to design vaccines. For more information, see the SNPGenie website and check out our review. Also stay tuned for a new publication introducing SNPGenie!