SoapNewCov

SoapNewCov: A efficient software tools to Calculate site depth of genome based soap List

chr/genome mean Depth and Coverage also will be given
Depth-GC Dis plot also can be given

1. Install

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Just [make] or [sh make.sh ] to compile this software.
the final software can be found in the Dir [bin/SoapNewCov]

For linux /Unix

        tar -zxvf  SoapNewCov-XXX.tar.gz
        cd SoapNewCov-XXX;                             # if Link do not work ,Try re-install  two  library
        cd src;                                        #【zlib and gzstream】 and copy them to the  library Dir
        make ; make clean                              # SoapNewCov-XX/src/include/zlib 
        ../bin/SoapNewCov                              # SoapNewCov-XX/src/include/gzstream

For macOS

#step1 :Should must re-install  two  library 【zlib and gzstream htslib】
              see  [zlib and gzstream] website 
#step2  :  # Copy these two library into Dirs 
              cp libz.a libz.so*  SoapNewCov-XX/src/include/zlib
              cp libgzstream.a  SoapNewCov-XX/src/include/gzstream
#step3  : 
              sh make.sh # or [make && make clean]

2. Example

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• 1. Calculate soap files

#To Calculate soap Depth with all mapping Read ,add Pare [-MinHit 10000 ]
 	./bin/SoapNewCov  -List  soap.list  -OutPut  out.depth.fa.gz   -Dict  Ref.fa -MinHit  10000
#To give out the genome Coverage,MeanDepth & Depth Dis , add Pare [ -Stat ]
 	./bin/SoapNewCov  -List  soap.list  -OutPut  out.depth.fa.gz  -Stat  -Dict Ref.dict
 	./bin/SoapNewCov  -List  soap.list  -OutPut  out.depth.fa.gz  -Stat  -Dict Ref.fa.gz

• 2. Calculate & Plot Depth-GC Dis Figure

# First Out Put the Depth-GC wig info with [ -OutWig ]
 	./bin/SoapNewCov  -List soap.list   -OutPut outFix   -Ref Ref.fa  -Stat -OutWig
# Second To Plot the Figure
# Must PreInstall R with library ggplot2,gridExtra,ggExtra

 	perl  bin/GC_Depth_Plot.pl  outFix.DepthGC.wig.gz  MaxDepth  OutFig

3. Introduction

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• Parameter description

    ./bin/SoapNewCov

        Usage: SoapNewCov  -List  <soap.list> -Dict <Ref.fa.gz>  -OutPut  <out.depth>

                -List      <str>     Input soap File List
                -Dict      <str>     Input Ref.fa or Ref.dict
                -OutPut    <str>     OutPut Depth info Fa file

                -Stat                Stat Coverage,MeanDepth & Depth Dis info
                -OutWig              Out Depth-GC wig info
                -Windows   <int>     Windows size for Depth-GC wig[10000]

                -MinHit    <int>     Filter the read bigger Mapping Hit [10]

                -help                Show this help [hewm2008 v1.10]

4. Results

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Introduction Result is the same the these two softwares

• SOAPcoverage
• Bamcoverage

5）Discussing

• email: hewm2008@gmail.com / hewm2008@qq.com
• join the QQ Group : 125293663

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