Analysis scripts for RAD-tag and whole genome shotgun sequencing using degraded DNA

Tin, Economo and Mikheyev, in prep

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.