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+NGSrich - Version 0.5.4
+Target enrichment performance for next-generation sequencing.
+
+
+Description:
+NGSrich is a tool for researchers concerned with target enrichment issues in next-generation sequencing.
+It evaluates the target enrichment performance of target regions given in BED format and outputs
+summary statistics, visualizations, and some additional files giving details on the analysis.
+
+
+---------------------------------------------------------------------------------------------------------
+
+
+Usage: 
+java NGSrich evaluate -r <readsFile> -u <genomeName> -t <target> 
+		      [(-a|-g) <annotation>] [ -s <sName> ] [-T <tmpDir>] [ -o <outDir>] [-p <poor> -h <high>][--no-details]
+
+		
+The program should be started from the bin directory of the software.
+Required arguments:
+       	<readsFile>:	Path to the read alignment file in SAM or BAM alignment format
+		     	(http://samtools.sourceforge.net/SAM-1.3.pdf)
+        <genomeName>: 	UCSC genome version name (e.g. 'hg19').
+       	<target>: 	Path to the target file in BED annotation format
+			(http://genome.ucsc.edu/FAQ/FAQformat.html#format1, 3 columns required)
+Optional arguments:
+	<annotation>: 	the local path of the annotation of the genome 
+			[default: genome annotation is downloaded from the site of the ucsc genome 
+				  browser and placed into the temporary directory of the sample.]
+	<sName>:	Name of the sample being processed - defaults to prefix of <readsFile>.
+        <tmpDir>:	Temporary directory - defaults to '/tmp'.
+       	<outDir>:	Output directory - defaults to '<pathToReadsFile>/enrichment'.
+        <poor>:		Coverage cutoff to define poorly covered genes - defaults to 2.
+       	<high>:		Coverage cutoff to define highly covered genes - defaults to 200.
+	--no-details:	Represses the computation of the evaluation details.	
+
+
+Output:
+1. The HTML file contains a report of the target enrichment results including
+   tables of poorly and highly covered genes (defined by cutoffs <poor> and <high>.
+   For vizualisation, plots are embedded in this document. The contents of this report
+   are actually based on an evaluation of the XML and BED files.
+2. The XML file contains the summary statistics for the enrichment performance.
+3. The BED file contains detailed coverage information for each single region specified in
+   the input target file.
+4. The WIG files (http://genome.ucsc.edu/goldenPath/help/wiggle.html) contain a per-base
+   description of the coverage on the target regions, one for the target regions specified in
+   the input target file and one for the whole genome (gaps are skipped). These files can be
+   used for visualization in a Genome Browser, e.g. at http://genome.ucsc.edu/cgi-bin/hgGateway.
+
+
+---------------------------------------------------------------------------------------------------------
+
+
+Several enrichment performance reports can be summarized by the command NGSrich-summarize.
+This should also be started from the bin directory of the software.
+
+Usage: java NGSrich summarize -r <inputIndexFile> -o <outDir> [ -p <poor> -h <high> ]
+
+Required arguments:
+       	<inputIndexFile>:	Text file with each line containing the output directory of
+				the report for one of the samples to be summarized.
+        <outDir>:		Output directory.
+
+Optional arguments:
+        <poor>:			Coverage cutoff to define poorly covered genes - defaults to 2.
+       	<high>:			Coverage cutoff to define highly covered genes - defaults to 200.
+
+
+Output:
+The HTML file contains a summary report and summarizing performance statistics for several
+target enrichment experiments. For each sample, the detailed performance report can be
+accessed by a hyperlink.
+
+
+---------------------------------------------------------------------------------------------------------
+
+
+Requirements:
+The NGSrich software runs only on 64-bit Linux. It requires an installation of R and the Java
+Runtime Environment (JRE), which are preinstalled on most Linux distributions. If not,
+please visit the official sites for detailed installation instructions.
+
+
+Contact:
+You can send an e-mail to the NGSrich mailing list at <NGSrich-users@lists.sourceforge.net>.
+Please tell us your experiences with the software itself and the documentation. We particularly welcome new 
+bug reports and suggestions for new or enhanced features.
+