Nice Advanced Tutorial: Overlapping Read Joiner

[holtgrewe]

The following task would be a nice advanced tutorial:

Input are two FASTQ files with reads that contain paired reads which length ~100bp, template size ~150-300bp. Many of the pairs will overlap.

The task is to take the read pairs and join overlapping reads into longer reads. In the case of conflicts, the higher-quality base should be chosen.

Various optional behaviour could be built in:

• if two conflicting bases with high quality (configurable threshold) conflict:
  • reject
  • convert to IUPAC alphabet

One existing tool is https://code.google.com/p/ea-utils/wiki/FastqJoin

[h-2]

@kreinert maybe something for the UGM?