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Repository picard
Name: picard
Owner: avowinkel
Synopsis: Picard SAM/BAM manipulation tools
SAM (Sequence Alignment/Map) is a generic format for storing large nucleotide sequence alignments. Picard comprises Java-based utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
Type: unrestricted
Revision: 1:5f1da1eadb39
This revision can be installed: True
Times cloned / installed: 574
Dependencies of this repository

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_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (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_picard_1_135 revision 865a9088fa2e owned by avowinkel

Name Version Type
R 3.1.2 package
picard 1.135 package

Contents of this repository

Name Description Version Minimum Galaxy Version
convert coordinate data into picard interval list format 1.135 any
assess validity of SAM/BAM dataset 1.135 any
convert Fastq data into unaligned BAM 1.135 any
collect metrics about the alignment of RNA to various functional classes of loci in the genome 1.135 any
Downsample a file to retain a subset of the reads 1.135 any
chart quality score distribution 1.135 any
ensure that all mate-pair information is in sync between each read and it's mate pair 1.135 any
sort SAM/BAM dataset 1.135 any
compute metrics for evaluating of whole genome sequencing experiments 1.135 any
charts the nucleotide distribution per cycle in a SAM or BAM dataset 1.135 any
chart distribution of base qualities 1.135 any
charts the GC bias metrics 1.135 any
merges multiple SAM/BAM datasets into one 1.135 any
plots distribution of insert sizes 1.135 any
merge alignment data with additional info stored in an unmapped BAM dataset 1.126.1 any
perform SAM/BAM grooming 1.135 any
assess sequence library complexity from read sequences 1.135 any
examine aligned records in BAM datasets to locate duplicate molecules 1.135 any
examine aligned records in BAM datasets to locate duplicate molecules 1.135 any
add or replaces read group information 1.135-gx-1 any
add comments to BAM dataset 1.135 any
extract reads and qualities from SAM/BAM dataset and convert to fastq 1.135 any
normalize fasta datasets 1.135 any
revert the original base qualities and add the mate cigar tag 1.135 any
revert SAM/BAM datasets to a previous state 1.135 any
include or exclude aligned and unaligned reads and read lists 1.135 any
reorder reads to match ordering in reference sequences 1.135 any
replace header in a SAM/BAM dataset 1.135 any
writes a file containing summary alignment metrics 1.135 any

Categories
SAM - Tools for manipulating alignments in the SAM format
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Variant Analysis - Tools for single nucleotide polymorphism data such as WGA