fqcheck: A new simple and efficient software to stat base and quality distribution of fq file
fqcheck v2.09
- Bug fixes: added missing pclose() calls in plot module; removed dead code (GetShiftQ, unused variables); fixed header guard in source file
- cycle_qual array dimension swapped for better cache locality
- Simplified q_err initialization (removed redundant pow computations)
- Makefile cleanup (removed non-existent include/lib directories)
- rapidgzip parallel decompression engine — up to 20× faster on large gzip files
- OpenMP parallel processing for Paired-End mode (both files processed concurrently)
- Batch buffered reading for reduced I/O overhead
- C++17 required (for rapidgzip)
Just make or sh make.sh to compile this software. The final binary can be found in bin/fqcheck
For linux /Unix and macOS
tar -zxvf fqcheckXXX.tar.gz
cd fqcheckXXX;
make ; make clean
./bin/fqcheck
Compile dependencies: g++ >= 7 (C++17), zlib, and rapidgzip source included under src/rapidgzip/
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- Parameter description:
Usage:fqcheck -InFq1 <in.fq> -OutStat1 <out.fqcheck> [options]
-InFq1 <str> File name of InFq Input
-OutStat1 <str> Prefix of OUT File name
-InFq2 <str> File name of InFq2 Input
-OutStat2 <str> Prefix of OUT File2 name
-Adapter1 <str> Input adapters fa file
-Adapter2 <str> Input adapters2 fa file
-help show this help[hewm2008 v2.09]-
- To Stat Fq file see the Dir [example]
# 2.1) Paire-End fq file
../bin/fqcheck -InFq1 B_1.fq.gz -InFq2 B_2.fq.gz -OutStat1 1 -OutStat2 2.fqcheck
# 2.2) Singel-End fq file
../bin/fqcheck -r B_1.fq.gz -c 1
# 2.3) Fq file withe adapters files
../bin/fqcheck -InFq1 B_1.fq.gz -OutStat1 1.fqcheck -InFq2 B_2.fq.gz -OutStat2 2 -Adapter1 iPE-3.fa -Adapter2 iPE-5.fa
some stat file will ouput.
Also if the system has gnuplot and convert commands installed, the following pictures will be output
- hewm2008@gmail.com / hewm2008@qq.com
- join the QQ Group : 125293663
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