OpenGene / pecheck

check paired-end FASTQ data integrity

pecheck

A tool to check paired-end FASTQ data integrity

usage

Just specify the read1 file by -i and the read2 file by -I. The input file can be gzipped (i.e. R1.fq.gz).

pecheck -i R1.fq -I R2.fq

A JSON report will be then generated. If the check is passed, the JSON result will be like:

{
	"result":"passed",
	"message":"",
	"read1_num":1000,
	"read2_num":1000,
	"read1_bases":108040,
	"read2_bases":109141
}

And if it's failed, the JSON result will be like:

{
	"result":"failed",
	"message":"Numbers of read1 and read2 are different",
	"read1_num":999,
	"read2_num":1000,
	"read1_bases":107923,
	"read2_bases":109141
}

The file name of the JSON report is pecheck.json by default, and it can be specified by -j. The JSON result is also printed on the terminal (STDOUT).

get pecheck

download binary

This binary is only for Linux systems: http://opengene.org/pecheck/pecheck

# this binary was compiled on CentOS, and tested on CentOS/Ubuntu
wget http://opengene.org/pecheck/pecheck
chmod a+x ./pecheck

or compile from source

# get source (you can also use browser to download from master or releases)
git clone https://github.com/OpenGene/pecheck.git

# build
cd pecheck
make

# Install
sudo make install