SWQC Features

The first versatile, distributed, and highly efficient sequencing data quality control software on the Sunway platform.

• Implemented a distributed FASTQ file IO framework that supports multi-threaded (de)compression based on the Sunway platform.

• The single-node version is 1.5-3 times faster than the fastest software on x86 platform and 5-20 times faster than the non-optimized Sunway version.

• The multi-node version achieves 65%-80% scalability on 16 nodes.

Build

SWQC can only support the next-generation Sunway platform.

Dependancy

• sw9gcc (7.1.0 or newer)
• zlib

Compilation

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

Simple usage

For next generation sequencing data

• For SE (not compressed)

./SWQC -i in1.fastq -o p1.fastq

• For SE (gzip compressed)

./SWQC -i in1.fastq.gz -o p1.fastq.gz

• For PE (not compressed)

./SWQC -i in1.fastq -I in2.fastq -o p1.fastq -O p2.fastq

• For PE (gzip compressed)

./SWQC -i in1.fastq.gz -I in2.fastq.gz -o p1.fastq.gz -O p2.fastq.gz

Options

For more help information, please refer to ./SWQC -h.

Visual output

We visualized the information before and after data filtering, and here is an example.