Degenerate Primer IDs and the Birthday Problem

Abstract

In PNAS, Jabara et al. (1) proposed an important approach to correct for recombination, allelic skewing, misincorporations, and sequencing errors in deep sequencing technologies. Their approach relies on each viral RNA template receiving a unique, randomly generated “Primer ID.” They were thus able to quantify template resampling by counting the repeated detection of each unique ID. Furthermore, they were able to exploit template resampling to correct for PCR errors, sequencing errors, and allelic skewing by only retaining consensus sequences where at least three reads shared a Primer ID. To attach a … [↵][1]1To whom correspondence should be addressed. E-mail: daniel.sheward{at}uct.ac.za. [1]: #xref-corresp-1-1