Homework 4 for Computer Science 362: Computational Biology.
This assignment is to create two programs. One which is called assembly and creates a De Bruijn Graph and Dot Graph for a given reads file. The second is called simulate and is meant to simulate a genome given a reads file with equal chance of mutation across all nucleotides.
Questions answered for the project:
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Our code is python and so doesn't need to compile. In the program, we import sys and random. For assemble.sh, we use graphviz in order to create the DOT file.
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There are no known bugs.
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We decided to utilise two classes for our assemble program: vertex and graph. These create essentially a graph via a dictionary.
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This project was written by Adam Ickler and Kristin Albright. We discussed the effect of larger files on the efficacy of the program with Layla Oesper.