Rapid Development and Distribution of Statistical Tools for High-Throughput Sequencing Data

WP1 Improved Read Mapping

OBJECTIVES
Mapping algorithms often only report the best match for a read and do not use information about matches with sub-optimal scores. For a read where the match with the highest alignment score lies in a region withlow coverage, but a second-best hit is in a highly covered area, the second hit may be a better candidate for the real position. Also, errors in the reference sequence can result in the top scoring mapped position being incorrect. We will address these problems by developing a new mapper which takes the read data coverage into account during the mapping process. With the increasing role of epigenetics for the understanding of molecular mechanisms, bisulfite sequencing to detect methylation of DNA is becoming increasingly common. However, aligning reads from bisulfite sequencing experiments remains a challenging task. We will develop improved methods which lead to significantly better results in less computation time.

 

PARTICIPATING PARTNERS
Genomatix (Lead Partner)
IIT