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Welcome to the Haplotype-Assembly wiki for the Haplotype Assembly Project for CS 124.

Description

This project will simulate creation of haplotype data and reads from the haplotypes. It will then run a greedy algorithm in order to get the original haplotype data back from the reads. There are two original haplotypes which need to be simulated. The two haplotypes are complementary (i.e. when the first is 110, the other is 001). Then, reads are taken from the simulated haplotypes. Reads are represented by 1s and 0s. The issue is that we will not know which reads correspond to which matrix. A matrix of reads is our input to the algorithm. The algorithm attempts to find the original haplotypes given the matrix of reads.

About Me

My name is Patrick Tan. I am currently a 3rd year Computer Science student attending UCLA taking CS 124.

Goal

I aim to code an algorithm to solve the haplotype assembly project and present the project in a clear manner.

Weekly Schedule

Week 6. Choose and work out a working algorithm Week 7. Code algorithm and test. Week 8. Create powerpoint and present. Week 9/10. Finish up any additions and clean up any bugs.

Weekly Update

Week 6.

1. Progress: I read and looked over some papers to think of an algorithm.
2. Plan: Start coding the algorithm.
3. Grade: A
4. Problems that came up: Coming up with an algorithm
5. Problems Solved: Creating the algorithm

Week 7.

1. Progress: Coded the haplotype assembly problem
2. Plan: Create presentation and present.
3. Grade: A
4. Problems that came up: Simulating the haplotypes with distances between SNPs
5. Problems Solved: Coded the entire algorithm