1. Develop a local read mapper for color-spaced reads.
2. To apply it to find viral integration sites in the human genome

For the local read mapper the goal is to use the the sequence space local aligner in SeqAn for all 4 possible color-space translations. Errors in the genome (sequence space) will be accounted for by the local sequence space mapper. Errors in the colorspace read will result in a discontinuous chain of local alignments in the 4 translated reads.

• Import the data → Done
• Convert color-spaced reads → Done
• Local readmapping with SWIFT-local → Done
• Take all the reads that did not map completely → 2 reasons:
  • Error in color-space
    • Convert the color-spaced read in all 4 possibilities
    • Map again
    • Construct a new read with the 4 possibilities
  • Read not in the genome
• Take all the reads that have parts which doesn't occur in the human genome → Done
• Map them to the viral genome → Done
• Find integration sites → Done
• Output file