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author timpalpant
date Mon, 13 Feb 2012 22:12:06 -0500
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1 = Java Genomics Toolkit
2
3 This is a collection of applications for genomics data processing, primarily high-throughput next-generation sequencing. There is a particular focus on processing data in Wiggle format, since many other tools already cover SAM, BAM, FastQ, etc. However, Wiggle/BigWig formats provide a compact way to store numerical data resulting from ChIP-seq and MNase-seq experiments. Common computations provided in this toolkit include adding, subtracting, dividing, multiplying, log-transforming, averaging, Z-scoring, and Gaussian smoothing Wig files.
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5 Tools may be run from the command-line, a simple Swing GUI, or from Galaxy (http://getgalaxy.org).
6
7 == Loading the Tools into Galaxy
8
9 TODO
10
11 == Using the ToolRunner GUI
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13 TODO
14
15 == Command-Line Usage
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17 Applications can be run on the command-line, and the toolRunner.sh script is provided for convenience. Calling any script without arguments will display the help, as well as the missing mandatory arguments:
18
19 $ > ./toolRunner.sh wigmath.AddWig
20 $ Usage: <main class> [options] Input files
21 $ Options:
22 $ * -o, --output Output file
23
24 Mandatory arguments are denoted with a (*).
25
26 Other tools require more input:
27
28 $ > ./toolRunner.sh ngs.Autocorrelation
29 $ Usage: <main class> [options]
30 $ Options:
31 $ * -i, --input Input file
32 $ * -l, --loci Genomic loci (Bed format)
33 $ -m, --max Autocorrelation limit (bp)
34 $ Default: 200
35 $ * -o, --output Output file
36
37 === Log transform a Wig file with base 2
38
39 $ > ./toolRunner.sh wigmath.LogTransform --input input.wig --base 2 --output output.log2.wig
40
41 == Java Genomics IO
42
43 Those wishing to write their own scripts may be interested in https://github.com/timpalpant/java-genomics-io, the toolkit upon which these applications are built.