Functionality wishlist

1. Add paired-end support for SPARTA
2. Add more modular approach to implementing different tools (perhaps through option specification?)
3. Include the ability to deal with batch effects in an efficient manner, requiring minimal user input
4. Support for other sequencing platforms as input (through adding support for SAM, BAM, FASTA, etc.)
5. Operon analysis
6. Definition of UTRs
7. Output read mapping files with normalized expression values
8. Non-reference based analysis