fqcheck: A new simple and efficient software to stat base and quality distribution of fq file
The new version will be updated and maintained in hewm2008/fqcheck, please click below Link to download the latest version
For linux/Unix static
you can use the statically compiled programs directly
chmod 755 ./bin/fqcheck
./bin/fqcheck
Just [make] or [sh make.sh ] to compile this software.the final software can be found in the Dir [bin/fqcheck]
For linux /Unix and macOS
tar -zxvf fqcheckXXX.tar.gz # if Link do not work ,Try re-install [zlib]library
cd fqcheckXXX; # [zlib] and copy them to the library Dir
make ; make clean # fqcheck-xx/src/include/zlib
./bin/fqcheck
Note: If fail to link,try to re-install the libraries zlib
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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 v2.08]-
- 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
- 📧 [email protected] / [email protected]
- join the QQ Group : 125293663
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