Repeat-aware Comparative Genome Assembly

The current high-throughput sequencing technologies produce gigabytes of data even when prokaryotic genomes are processed. In a subsequent assembly phase, the generated overlapping reads are merged, ideally into one contiguous sequence. Often, however, the assembly results in a set of contigs which need to be stitched together with additional lab work. One of the reasons why the assembly produces several distinct contigs are repetitive elements in the newly sequenced genome. While knowing order and orientation of a set of non-repetitive contigs helps to close the gaps between them, special care has to be taken for repetitive contigs. Here we propose an algorithm that orders a set of contigs with respect to a related reference genome while treating the repetitive contigs in an appropriate way.