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1 NGSrich - Version 0.5.4
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2 Target enrichment performance for next-generation sequencing.
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3
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4
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5 Description:
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6 NGSrich is a tool for researchers concerned with target enrichment issues in next-generation sequencing.
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7 It evaluates the target enrichment performance of target regions given in BED format and outputs
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8 summary statistics, visualizations, and some additional files giving details on the analysis.
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9
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10
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11 ---------------------------------------------------------------------------------------------------------
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12
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13
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14 Usage:
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15 java NGSrich evaluate -r <readsFile> -u <genomeName> -t <target>
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16 [(-a|-g) <annotation>] [ -s <sName> ] [-T <tmpDir>] [ -o <outDir>] [-p <poor> -h <high>][--no-details]
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17
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18
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19 The program should be started from the bin directory of the software.
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20 Required arguments:
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21 <readsFile>: Path to the read alignment file in SAM or BAM alignment format
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22 (http://samtools.sourceforge.net/SAM-1.3.pdf)
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23 <genomeName>: UCSC genome version name (e.g. 'hg19').
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24 <target>: Path to the target file in BED annotation format
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25 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1, 3 columns required)
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26 Optional arguments:
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27 <annotation>: the local path of the annotation of the genome
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28 [default: genome annotation is downloaded from the site of the ucsc genome
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29 browser and placed into the temporary directory of the sample.]
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30 <sName>: Name of the sample being processed - defaults to prefix of <readsFile>.
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31 <tmpDir>: Temporary directory - defaults to '/tmp'.
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32 <outDir>: Output directory - defaults to '<pathToReadsFile>/enrichment'.
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33 <poor>: Coverage cutoff to define poorly covered genes - defaults to 2.
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34 <high>: Coverage cutoff to define highly covered genes - defaults to 200.
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35 --no-details: Represses the computation of the evaluation details.
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36
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37
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38 Output:
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39 1. The HTML file contains a report of the target enrichment results including
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40 tables of poorly and highly covered genes (defined by cutoffs <poor> and <high>.
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41 For vizualisation, plots are embedded in this document. The contents of this report
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42 are actually based on an evaluation of the XML and BED files.
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43 2. The XML file contains the summary statistics for the enrichment performance.
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44 3. The BED file contains detailed coverage information for each single region specified in
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45 the input target file.
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46 4. The WIG files (http://genome.ucsc.edu/goldenPath/help/wiggle.html) contain a per-base
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47 description of the coverage on the target regions, one for the target regions specified in
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48 the input target file and one for the whole genome (gaps are skipped). These files can be
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49 used for visualization in a Genome Browser, e.g. at http://genome.ucsc.edu/cgi-bin/hgGateway.
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50
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51
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52 ---------------------------------------------------------------------------------------------------------
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53
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54
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55 Several enrichment performance reports can be summarized by the command NGSrich-summarize.
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56 This should also be started from the bin directory of the software.
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57
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58 Usage: java NGSrich summarize -r <inputIndexFile> -o <outDir> [ -p <poor> -h <high> ]
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59
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60 Required arguments:
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61 <inputIndexFile>: Text file with each line containing the output directory of
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62 the report for one of the samples to be summarized.
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63 <outDir>: Output directory.
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64
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65 Optional arguments:
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66 <poor>: Coverage cutoff to define poorly covered genes - defaults to 2.
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67 <high>: Coverage cutoff to define highly covered genes - defaults to 200.
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68
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69
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70 Output:
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71 The HTML file contains a summary report and summarizing performance statistics for several
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72 target enrichment experiments. For each sample, the detailed performance report can be
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73 accessed by a hyperlink.
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74
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75
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76 ---------------------------------------------------------------------------------------------------------
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77
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78
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79 Requirements:
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80 The NGSrich software runs only on 64-bit Linux. It requires an installation of R and the Java
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81 Runtime Environment (JRE), which are preinstalled on most Linux distributions. If not,
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82 please visit the official sites for detailed installation instructions.
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83
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84
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85 Contact:
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86 You can send an e-mail to the NGSrich mailing list at <NGSrich-users@lists.sourceforge.net>.
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87 Please tell us your experiences with the software itself and the documentation. We particularly welcome new
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88 bug reports and suggestions for new or enhanced features.
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89
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