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Repository alfa
Name: alfa
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.
Type: unrestricted
Revision: 46:5d745637f045
This revision can be installed: True
Times cloned / installed: 286
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Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
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_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_readline_6_3 revision ca1a9400d4e1 owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_xz_5_0_5 revision 944f93d45594 owned by iuc (prior install required)
Repository package_sqlite_3_8_3 revision c8a5c11cc921 owned by iuc (prior install required)
Repository package_gdbm_1_11 revision ed2537bccffc owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_libtool_2_4 revision 7f67694b167c owned by iuc (prior install required)
Repository package_python_2_7_numpy_1_9 revision f24fc0b630fc owned by iuc (prior install required)
Repository package_freetype_2_5_2_matplotlib_fix revision 26586565bc22 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_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
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_bedtools_2_24 revision 3416a1d4a582 owned by iuc

Name Version Type
matplotlib 1.4 package
bedtools 2.24 package
samtools 1.2 package

Contents of this repository

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
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Visualization - Tools for visualizing data