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RabbitSAlign: GPU acceleration of short read alignment for heterogeneous multicore platforms

RabbitSAlign is a GPU-accelerated short-read aligner based on strobealign. It doubles the processing speed on real biological data by utilizing GPU to accelerate the extending phase and optimizing inefficient operations in the seeding process.

Dependancy

  • gcc 9.4.0 or newer
  • nvcc 12.0 or newer

Installation

git clone https://github.com/RabbitBio/RabbitSAlign
cd RabbitSAlign
bash build.sh <path-to-cuda-installation-directory> <GPU-compute-capability>
(eg: bash build.sh /usr/local/cuda 86)

The resulting binary is in build/rabbitsalign.

Usage

Detailed usage can refer to the strobealign. RabbitSAlign can share the index file (.sti) with strobealign.

Note: If there is an error saying GPU out of memory, you can adjust the STREAM_BATCH_SIZE variable in src/gasal2_ssw.h, which is proportional to the size of the GPU memory.