Fast and Accurate mapping of Next Generation Sequencing Data

Abstract

Next Generation Sequencing (NGS) has opened up new possibilities in genomic studies. However, studying the vast amounts of data produced by these technologies present several challenges. In many applications, millions of reads will to be mapped to very large genomes of size around 3 GB. Furthermore, the mapping needs to take into account errors in the form of mismatches and indels. Burrows-Wheeler transform (BWT) is a data structure used prominently by sequence aligners. In this thesis I introduce BWT based algorithms to efficiently and accurately align NGS data.