Order of Things To Deal With

1. Finish merging branches together and speeding up the library creation step.

2. Correct autocomplete -- in the process make it so the 1st 100 bp are in the complete gene that is being blasted against.

3. Make it so the contig from the previous iteration is used in the assembly

4. Remove paired end option so people can run it if they don't have a paired end library.

5. Output the number of blast hits in the result file.

FOR JULIE:

1. Figure out optimal number of processors to run on the cluster.
2. Test paired end tweak the velvet line from paired to non paired
3. tblastn for phum next