There are two components to this analysis, each with its own code and readme:
- RAD-tag sequencing of ant libraries on the MiSeq
- Whole genome shotgun of Hawaiian fruitfly sequencig using MiSeq and HiSeq
Note: these files were designed to be run on the Okinawa Institute of Science and Technology SGE-based cluster (tombo), and may refer to specific software configurations found there. However, the code can be easily adapted to other environments.