qualimap - 1.0.1
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<joachim.jacob@vib.be>

SUMMARY
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Qualimap examines sequencing alignment data in SAM/BAM files and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis. 

http://qualimap.bioinfo.cipf.es/

Garcia-Alcalde et.al, (2012) Qualimap: evaluating next generation sequencing aligmnent data,
Bioinformatics. doi: 10.1093/bioinformatics/bts503 
	  
REQUIREMENTS AND INSTALLATION
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Install this tool in your Galaxy via the Toolshed

   ) Required dependencies:
	- Qualimap available in the PATH
	- Perl 
	- Perl core module File::Temp and File::Basename
	- Perl module Log::Log4perl	

   ) Integration into Galaxy
	Please use the toolshed

DETAILS AND ISSUES
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   ) Qualimap suite provide various quality control tools to apply 
     after mapping. Only bamqc is provided in this first version
   ) bamqc reports various statistics of an alignment.

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