This repository contains the source code of the paper "Accelerating Sequence-to-Graph Alignment on Heterogeneous Processors", by Zonghao Feng and Prof. Qiong Luo.
Execute the following command to compile the project:
# Compile
make all
# Print debug information
make debug
Parameters of the program:
./bin/hga [-grmnodbt]
-g: graph file
-r: read file
-m: match score
-n: mismatch score
-o: gap penalty
-d: number of GPUs
-b: number of thread blocks
-t: number of threads per block
The suggested parameters for RTX 2080 Ti GPU are 68 thread blocks and 128 threads per block.
Scalability evaluation:
./bin/scale.sh
- Extend to GPU clusters to support larger datasets
- Support more genome graph formats
- Intra-sequence parallelization