Algorithmic Bioinformatics

Sven-Léon Kuchenbecker

Handling ambiguity in read mapping applications

Academic Advisor: Knut Reinert
Discipline: Bioinformatik
Degree: Master of Science (M.Sc.)
Degree: Oct 20, 2011
Status: finished


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. 



[1] Kececioglu, Yu: Separating repats in DNA sequence assembly.

[2] Tammi et al. : Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs, Bioinformatics 18, 2002, 379-388

[3] Stephan Aiche: Separation of repeats in shotgun assembly data, MSc thesis.