HGA (Heterogeneous Graph Aligner)

This repository contains the source code of the paper "Accelerating Sequence-to-Graph Alignment on Heterogeneous Processors", by Zonghao Feng and Prof. Qiong Luo.

Build

Execute the following command to compile the project:

# Compile
make all

# Print debug information
make debug

Run

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 

Ongoing work

• Extend to GPU clusters to support larger datasets
• Support more genome graph formats
• Intra-sequence parallelization