SWBWA

A high-accuracy and high-performance short read aligner optimized for the next-generation Sunway platform.

Features

• Redesigned a parallel framework tailored for Sunway’s heterogeneous architecture, with software prefetching and memory access optimizations in bigshare mode.

• Achieves up to 330× speedup over the unoptimized single-thread version, and 1.2–1.4× faster than bwamem on a dual-socket 48-core x86 server with nearly identical results.

Build

SWBWA can only support the next-generation Sunway platform.

Dependency

• sw9gcc (7.1.0 or newer)
• zlib

Compilation

git clone https://github.com/RabbitBio/SWBWA.git
cd SWBWA
make -j4

Simple usage

Index the reference

SWBWA is compatible with index files generated by bwamem.

./SWBWA index ref.fa

Align reads

• Single-end:

./SWBWA mem ref.fa reads.fq -o aln.sam

• Paired-end:

./SWBWA mem ref.fa read1.fq read2.fq -o aln.sam

Options

For more help information, please refer to:

./SWBWA mem