The cross-assembly consists of two rounds, one for each family individually and the the cross-assembly for all families.
To run the first round of assembly run: Wrapper_CrossAssembly_Malawi1.pl F3 > Log_Ma_F3.txt
To Run de second run of assembly, run:
Wrapper_CrossAssembly_Malawi2.pl F22 > Log_Ma2_F22.txt
Third party software needed: cd-hit-est runAssembly fr-hit makeblastdb / blastn phrap
Is designed for a cluster environment running in SGE job scheduler.