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.


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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.


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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.


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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.