CallSim: Evaluation of Base Calls Using Sequencing Simulation.

ABSTRACT: Accurate base calls generated from sequencing data are required for downstream biological interpretation, particularly in the case of rare variants. CallSim is a software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. The algorithm processes a single read using a Monte Carlo approach to sequencing simulation, not dependent upon information from any other read in the data set. Three examples from general read correction, as well as from error-or-variant classification, demonstrate its effectiveness for a robust low-volume read processing base corrector. Specifically, correction of errors in Ion Torrent reads from a study involving mutations in multidrug resistant Staphylococcus aureus illus

SUBMITTER: Morrow JD 

PROVIDER: S-EPMC4393072 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature