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fqcheck: A new simple and efficient software to stat base and quality distribution of fq file

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fqcheck

fqcheck: A new simple and efficient software to stat base and quality distribution of fq file

1) Install


The new version will be updated and maintained in hewm2008/fqcheck, please click below Link to download the latest version

hewm2008/fqcheck

Download

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

2) Example of fqcheck


    1. 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 v2.07]
    1. 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

3) Results


some stat file will ouput.
Also if the system has gnuplot and convert commands installed, the following pictures will be output

base.png

qual.png

4) Discussing


######################swimming in the sky and flying in the sea ########################### ##

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fqcheck: A new simple and efficient software to stat base and quality distribution of fq file

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  • C++ 79.6%
  • C 14.9%
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  • Makefile 1.3%