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Next-generation sequencing algorithms: from read mapping to variant detection

Next-Generation-Sequencing (NGS) has brought on a revolution in sequence analysis with its broad spectrum of applications ranging from genome resequencing to transcriptomics or metagenomics, and from fundamental research to diagnostics. The tremendous amounts of data necessitate highly efficient computational analysis tools for the wide variety of NGS applications. This thesis addresses a broad range of key computational aspects of resequencing applications, where a reference genome sequence is known and heavily used for interpretation of the newly sequenced sample. It presents tools for read mapping and benchmarking, for partial read mapping of small RNA reads and for structural variant/indel detection, and finally tools for detecting and genotyping SNVs and short indels. Our tools efficiently scale to large NGS data sets and are wellsuited for advances in sequencing technology, since their generic algorithm design allows handling of arbitrary read lengths and variable error rates. Furthermore, they are implemented within the robust C++ library SeqAn, making them open-source, easily available, and potentially adaptable for the bioinformatics community. Among other applications, our tools have been integrated into a large-scale analysis pipeline and have been applied to large datasets, leading to interesting discoveries of human retrocopy variants and insights into the genetic causes of X-linked intellectual disabilities.