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PAR-CLIP Read MApper toolkit. Useful tools for short and error prone sequence read handling.

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PARA-suite toolkit

PAR-CLIP Analyzing suite. Useful tools for short and error prone sequence read handling. Note, that the PARA-suite addon of the Burrows-Wheeler Aligner (BWA) is necessary for the mapping tool of the PARA-suite.

For more information on the usage please see "Manual.pdf".

Installation

git clone https://github.com/akloetgen/PARA-suite.git
cd PARA-suite/bin/
java -jar parasuite.jar setup --parasuite $myPATH_TO_PARASUITE

The 3rd installation step sets the path to the binary-folder of the PARA-suite alignment algorithm to make it accessible for the PARA-suite toolkit. Therefore, make sure the PARA-suite alignment algorithm (https://github.com/akloetgen/PARA-suite_aligner) is installed correctly.

Build instructions

git clone https://github.com/akloetgen/PARA-suite.git
cd PARA-suite/src/
ant -buildfile PARAsuite_build.xml
cd ../bin/
java -jar parasuite.jar setup --parasuite $myPATH_TO_PARASUITE

Requirements

Getting help

java -jar parasuite.jar --help

If the alignment aborts with an unspecified error, please forward us the alignment log-file (should be named $your_output.log).

Testdata

chmod u+x examples.sh examples_remove_temp.sh
./examples.sh
./examples_remove_temp.sh

If you have installed the Perl CPAN Math::Random package locally, you have to specify the path to the installed package in the examples.sh script at the top like in the following example: myPathToMathRandom=~/.cpan/installed/lib/perl

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