DuoHash: Improving Spaced k-mer Extraction and Hash Encoding for Bioinformatics Applications

Methods

The DuoHash library provides two classes: DuoHash and DuoHash_multi for handling one or multiple spaced seeds, respectively. The methods of the first class are

• GetEncoding_naive(),
• GetEncoding_FSH(),
• and GetEncoding_ISSH().

The methods of the second class are

• GetEncoding_naive(),
• GetEncoding_FSH(),
• GetEncoding_ISSH(),
• GetEncoding_FSH_multi(),
• GetEncoding_MISSH_v1(),
• GetEncoding_MISSH_col(),
• GetEncoding_MISSH_col_parallel(),
• and GetEncoding_MISSH_row().

Both classes share the PrintFASTA() method for saving the resulting spaced k-mers to a file and other methods for handling the various parameters.

Each GetEncoding_<...>() method has four implementations. The first is for the extraction of spaced k-mer and their encoding only, the second allows post-processing of encodings to calculate forward and reverse hashing, the third allows post-processing of encodings for conversion into strings, and the fourth combines the two previous options.

Installation

Make sure CMake is installed on the system.

Download the repository using

$ git clone https://github.com/leonardoGemin/DuoHash.git

and build the library with

$ make build

This will install build/libDuoHash.a in the project's directory.

Usage

To use DuoHash in a C++ project:

• Import DuoHash in the code using #include <DuoHash.h>
• Add the include directory (pass -I./include to the compiler)
• Link the code with libDuoHash.a (pass -L./build -lDuoHash to the compiler)
• Compile your code with g++-13, -std=c++0x (and preferably -O3), and -fopenmp enabled

Example

Compile example/main.cpp file with

$ cd example
$ g++-13 -std=c++0x -O3 -fopenmp -I../include -L../build -lDuoHash -o main main.cpp

Thesis

Link to my Master Thesis: Gemin_Leonardo.pdf