Repository alfa
Name: alfa
Owner: biocomp-ibens
Synopsis: Plot the distribution of the genomic features captured by aligned reads
ALFA provides a global overview of features distribution composing New Generation Sequencing dataset(s).
Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.
Content homepage: https://github.com/biocompibens/ALFA/
Development repository: https://github.com/biocompibens/ALFA/tree/master/Galaxy_toolshed_repositories/alfa
Link to this repository: https://toolshed.g2.bx.psu.edu/view/biocomp-ibens/alfa/e360f840a92e
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/biocomp-ibens/alfa
Type: unrestricted
Revision: 0:e360f840a92e
This revision can be installed: True
Times cloned / installed: 304
Dependencies of this repository

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Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_python_2_7_numpy_1_9 revision f24fc0b630fc owned by iuc (prior install required)
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Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 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)
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Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
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Repository package_libtool_2_4 revision 7f67694b167c owned by iuc (prior install required)
Repository package_bedtools_2_24 revision 3416a1d4a582 owned by iuc

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
bedtools 2.24 package
matplotlib 1.4 package
samtools 1.2 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
- Plot the distribution of the genomic features captured by aligned reads 0.1.0 16.01

Categories
Graphics - Tools producing images
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Visualization - Tools for visualizing data