SMARTAptamerPy

Python implementation of SMART Aptamer from this paper.

This will allow others to use it to make modifications to it easier.

Dependencies

The following programs are required to run this program:

• RNAfold
• MCL
• QGRS

Instructions

1. Install the dependencies listed above. *(for QGRS, we need clone their repo, build the code and then move the qgrs-cpp folder into the folder for this project)
2. Install libraries in requirements.txt
3. Put fastq files for each round in data/targ_fastq_?
4. Write name of each round file in data/targ_fastq_? in seperate lines without .fastq
5. Write each primer in a separate line in data/targ_primers.txt
6. Run fastqcleaner.py
7. Run fastq2txt.py
8. Run main.py