SUP: a probabilistic framework to propagate genome sequence uncertainty, with applications.

ABSTRACT: Genetic sequencing is subject to many different types of errors, but most analyses treat the resultant sequences as if they are known without error. Next generation sequencing methods rely on significantly larger numbers of reads than previous sequencing methods in exchange for a loss of accuracy in each individual read. Still, the coverage of such machines is imperfect and leaves uncertainty in many of the base calls. In this work, we demonstrate that the uncertainty in sequencing techniques will affect downstream analysis and propose a straightforward method to propagate the uncertainty. Our method (which we have dubbed Sequence Uncertainty Propagation, or SUP) uses a probabilistic matrix representation of individual sequences which incorporates base quality scores as a measure of uncert

SUBMITTER: Becker D 

PROVIDER: S-EPMC10124968 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature