Read Mapping Project
Description
This project implements a fast and accurate read mapping algorithm for DNA sequences using C++.
The following algorithms are used:
- Suffix array construction using the SAIS algorithm.
- Smith-Waterman algorithm for string alignment.
Environment
I developed the project on an M1 Macbook Pro using Apple's clang g++ compiler (version 14.0.3). The project should be able to be compiled on any system with a C++ compiler that supports C++17.
Compiling
To compile the project, run the following command in the project directory:
mkdir build
cd build
cmake ..
make
cd ..Two binaries will be generated:
debug- a debug build of the project, with debug symbols and no optimizations.release- a release build of the project, with -O3 optimizations. Please use this binary to process large inputs.
Running
The program takes two arguments: the path to the reference genome, and the path to the reads file. Under the project directory, run the following command:
mkdir output
./build/release <path to reference genome> <path to reads file>The output will be written to output/output.txt.
To reformat the output to the submission .zip format, run the following bash script:
./format_output.shReferences and Acknowledgements
When developing the project, I acknowledge using the following sources in learning relevant algorithms and adapting codes from them.
- SAIS algorithm for suffix array construction.
- SAIS algorithm C++ implementation.
- C++17 parallelized std algorithms for Apple clang compiler.
- Smith-Waterman Algorithm for string alignment.