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Repository picard
Name: picard
Owner: devteam
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.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/picard
Type: unrestricted
Revision: 11:efc56ee1ade4
This revision can be installed: True
Times cloned / installed: 12445
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_136 revision 3e9c24e5325b owned by devteam

Name Version Type
R 3.1.2 package
picard 1.136 package

Contents of this repository

Name Description Version Minimum Galaxy Version
examine aligned records in BAM datasets to locate duplicate molecules 1.136.0 any
merge alignment data with additional info stored in an unmapped BAM dataset 1.136.0 any
Downsample a file to retain a subset of the reads 1.136.0 any
writes a file containing summary alignment metrics 1.136.1 any
convert coordinate data into picard interval list format 1.136.0 any
add or replaces read group information 1.136.0 any
plots distribution of insert sizes 1.136.0 any
chart distribution of base qualities 1.136.0 any
revert SAM/BAM datasets to a previous state 1.136.0 any
convert Fastq data into unaligned BAM 1.136.0 any
sort SAM/BAM dataset 1.136.1 any
compute metrics for evaluating of whole genome sequencing experiments 1.136.0 any
ensure that all mate-pair information is in sync between each read and it's mate pair 1.136.0 any
add comments to BAM dataset 1.136.0 any
include or exclude aligned and unaligned reads and read lists 1.136.0 any
normalize fasta datasets 1.136.0 any
assess sequence library complexity from read sequences 1.136.0 any
perform SAM/BAM grooming 1.136.0 any
collect metrics about the alignment of RNA to various functional classes of loci in the genome 1.136.0 any
charts the GC bias metrics 1.136.0 any
replace header in a SAM/BAM dataset 1.136.0 any
merges multiple SAM/BAM datasets into one 1.136.0 any
charts the nucleotide distribution per cycle in a SAM or BAM dataset 1.136.0 any
revert the original base qualities and add the mate cigar tag 1.136.0 any
assess validity of SAM/BAM dataset 1.136.0 any
extract reads and qualities from SAM/BAM dataset and convert to fastq 1.136.0 any
reorder reads to match ordering in reference sequences 1.136.0 any
examine aligned records in BAM datasets to locate duplicate molecules 1.136.0 any
chart quality score distribution 1.136.0 any

Categories
SAM - Tools for manipulating alignments in the SAM format