im-mou / gpu-kmer-counter

Implementación del algoritmo para contar K-mers en una secuencia genética usando GPUs.

im-mou/gpu-kmer-counter

Speeding up the algorithm to count K-mers in a genetic sequence using GPUs.

Abstract

K-mer counting is a process with the goal of creating a histogram of all possible combinations of length k for an input string S. From an algorithmic point of view, counting k-mers in a string seems like a very simple task but with recent advances in sequencing technology, more and more sequencing machines are generating a large amount of data in a very short time and makes the simple task of generating a histogram a challenge. In recent years, the performance of k-mer counting algorithms has improved significantly, and there has been much interest in using graphics processing units (GPUs) to accomplish the task of counting k-mers. The fundamental purpose of this research is to analyze different algorithms to count the number of occurrences in a sequence with different k-mer settings and subsequently to optimize and speed up one of the algorithms by using GPUs.

Source repository

Source code repository: lh3/kmer-cnt
This repository contains all the the source code of the diferent implementations that has been used and experimented with for this research.

Instructions to use and test the implementations

git clone https://github.com/im-mou/gpu-kmer-counter
cd gpu-kmer-counter
make

Download and parse the dataset for different implementations

wget https://github.com/lh3/kmer-cnt/releases/download/v0.1/M_abscessus_HiSeq_10M.fa.gz
./parse-data ./M_abscessus_HiSeq_10M.fa.gz

Execute implementations

By default all these script execute the code with k-mer length of 32. If you choose to experiment with a diferent k size, you can edit the corresponding slurm file and uncomment the line with the desired k-length.

Secuential: kc-c1-fast.c

sbatch ./slurm_scripts/slurm-kc-c1-fast.sub

Parallel: cuda-fast.c - Best implementation

sbatch ./slurm_scripts/slurm-cuda-fast.sub

Parallel: cuda-dumb.c - Pretty dumb. Non-atomic, experimental purpose only.

sbatch ./slurm_scripts/slurm-cuda-dumb.sub

Scripts

The two properly working final sequential and parallel implementation with the correct outputs are the following:

• kc-c1-fast.c
• cuda-fast.cu