An Analysis Pipeline and its Application on the Cucurbita pepo Genome

First insights into the genome of Cucurbita pepo are presented in this thesis. 15.67 percent of the 2,349,855 sequence reads generated with Roche’s 454 Pryosequencer received a classification in preprocessing. Of the remaining sequence reads 38.82% were classified as repeats, 11.08 percent as gene coding region, 7.08 percent as chloroplast and 5.39 percent as mitochondrial sequences. A comparison with the genome of cucumber reinforces this distribution. Moreover, this thesis describes an automated analysis pipeline for genome analyses. It is equipped with a set of newly developed components to perform whole genome analyses with next generation sequencing datasets, to store the obtained results into a database and to visualize them on a web interface. Comparisons with state of the art analysis pipelines show that its visualization capabilities and automatic input checker are rare but very helpful features.