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Repository contra
Name: contra
Owner: fcaramia
Synopsis: tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. GVL. PeterMac
CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. CONTRA calls copy number gains and losses for each target region with key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. It takes standard alignment formats (BAM/SAM) and output in variant call format (VCF 4.0) for easy integration with other next generation sequencing analysis package. 
Link to this repository: https://toolshed.g2.bx.psu.edu/view/fcaramia/contra/0bf826f62f04
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/fcaramia/contra
Type: unrestricted
Revision: 27:0bf826f62f04
This revision can be installed: True
Times cloned / installed: 561
Dependencies of this repository

Repository dependencies - installation of these additional repositories is required
Repository package_readline_6_2 revision 5313ca2fbce6 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_cairo_1_12_14 revision cd2ed5717e38 owned by devteam (prior install required)
Repository package_pixman_0_32_4 revision 93cd8e03820c owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision a65217367e4a owned by devteam (prior install required)
Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_pixman_0_32_4 revision 93cd8e03820c owned by devteam (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision a65217367e4a owned by devteam (prior install required)
Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision 1e86d1cf79a4 owned by iuc (prior install required)
Repository package_libxml2_2_9_1 revision 45b16a3ab504 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_samtools_0_1_18 revision 171cd8bc208d owned by devteam

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
R 3.0.3 package
bedtools 2.17.0 package
contra 2.0.4 package
samtools 0.1.18 package

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
: Copy Number Analysis for Targeted Resequencing 1.0.0 any
: Control files for Contra 1.0.0 any

Categories
Genomic Interval Operations - Tools for operating on genomic intervals
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Statistics - Tools for generating statistics