Handling ambiguity in read mapping applications
This thesis deals with the problem of post-processing read mapping data to resolve ambiguously mapped reads, i.e. regions within the multi-alignment produced by a read mapper that are covered by reads that actually originate from different regions. For that purpose, an algorithm work flow was designed, implemented and evaluated for different read mapping scenarios.
 Kececioglu, Yu: Separating repats in DNA sequence assembly.
 Tammi et al. : Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs, Bioinformatics 18, 2002, 379-388
 Stephan Aiche: Separation of repeats in shotgun assembly data, MSc thesis.