Add to ORKGk-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the most popular tools for k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. We achieved 4.03x speedup using one GTX 1080 Ti with one CPU (Xeon E5-2603) thread and 5.88x speedup using one GPU with four CPU threads over KMC2 running on a single CPU thread. This speedup is significant because accelerating k-mer counting is challenging due to reasons like serialized portions of code and overhead of disk operations
Genome analysis benefits precise medical care, wildlife conservation, pandemic treatment, e.g., COVI...
AbstractGenotype imputation is an important approach for improving the power of genome-wide associat...
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and i...
k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the...
Next-generation sequencing (NGS) technology has led to a rapid growth in the amount of genomic infor...
The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic ...
Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide dat...
Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide dat...
k-mer counting is an essential algorithm found in many genomic related processes. It may seem like a...
Abstract Background A basic task in bioinformatics is the counting of k-mers in genome sequences. Ex...
A fundamental step in many bioinformatics computations is to count the frequency of fixed-length seq...
Over the past few years, DNA sequencing technology has been advancing at such a fast pace that compu...
BarraCUDA uses CUDA graphics cards to map DNA reads to the human genome. Previously its software sou...
Recent advances in DNA sequencing technology have opened new doors for scientists to use genomic dat...
The idea of using a graphics processing unit (GPU) for more than simply graphic output purposes has ...
Genome analysis benefits precise medical care, wildlife conservation, pandemic treatment, e.g., COVI...
AbstractGenotype imputation is an important approach for improving the power of genome-wide associat...
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and i...
k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the...
Next-generation sequencing (NGS) technology has led to a rapid growth in the amount of genomic infor...
The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic ...
Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide dat...
Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide dat...
k-mer counting is an essential algorithm found in many genomic related processes. It may seem like a...
Abstract Background A basic task in bioinformatics is the counting of k-mers in genome sequences. Ex...
A fundamental step in many bioinformatics computations is to count the frequency of fixed-length seq...
Over the past few years, DNA sequencing technology has been advancing at such a fast pace that compu...
BarraCUDA uses CUDA graphics cards to map DNA reads to the human genome. Previously its software sou...
Recent advances in DNA sequencing technology have opened new doors for scientists to use genomic dat...
The idea of using a graphics processing unit (GPU) for more than simply graphic output purposes has ...
Genome analysis benefits precise medical care, wildlife conservation, pandemic treatment, e.g., COVI...
AbstractGenotype imputation is an important approach for improving the power of genome-wide associat...
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and i...