With the rise in prominence of biological research using new short-read DNA sequencing
technologies comes the need for new techniques for aligning and assigning these reads to
their genomic location of origin. Until now, methods for allocating reads which align with equal or
similar fidelity to multiple genomic locations have not been model-based, and have tended to ignore
potentially informative data. Here, we demonstrate that existing methods for assigning ambiguous
reads can produce biased results. We then present new methods for allocating ambiguous reads to
the genome, developed within a framework of statistical modeling, which show promise in alleviating
these biases, both in simulated and real data.