A tool designed to provide high-speed scalable quality control for sequencing data which can take full advantage of modern hardware. It includes a variety of function modules and supports different sequencing technologies (Illumina, Oxford Nanopore, PacBio). Fastp2 achieves speedups between one and two orders-of-magnitude compared to other state-of-the-art tools.

• For single end data (not compressed)

rabbit_qc -w nthreads -i in.fq -o out.fq

• For paired end data (gzip compressed)

rabbit_qc -w nthreads -i in.R1.fq.gz -I in.R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz

rabbit_qc -w nthreads -D -i in.fq

A more efficient strategy to process large gzip compressed FASTQ files is to decompress files using pugz and then process them using Fastp2. Pugz has been integrated into Fastp2 project.

cd Fastp2/pugz && make asserts=0
./gunzip -t nthreads in.fq.gz

For more help information, please refer to rabbit_qc -h.

If -w opition is not specified, Fastp2 will set working thread number to total CPU cores - 2. By default, the HTML report is saved to Fastp2.html (can be specified with -h option), and the JSON report is saved to Fastp2.json (can be specified with -j option).

Fastp2 suports all fastp options for short read quality control and all NanoQC optiions for long read quality control. For details please refer to fastp and NanoQC.

Fastp2 creates reports in both HTML and JSON format.

For Linux and OSX:

cd Fastp2 && make

cd Fastp2 && make