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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: 26:9ffcddf6f9c0
This revision can be installed: True
Times cloned / installed: 17042

Contents of this repository

Name Description Version Minimum Galaxy Version
add comments to BAM dataset 2.18.2.1 16.01
add or replaces read group information 2.18.2.1 16.01
convert coordinate data into picard interval list format 2.18.2.1 16.01
perform SAM/BAM grooming 2.18.2.1 16.01
writes a file containing summary alignment metrics 2.18.2.1 16.01
charts the nucleotide distribution per cycle in a SAM or BAM dataset 2.18.2.1 16.01
charts the GC bias metrics 2.18.2.1 16.01
plots distribution of insert sizes 2.18.2.1 16.01
collect metrics about the alignment of RNA to various functional classes of loci in the genome 2.18.2.1 16.01
Collect metrics to quantify single-base sequencing artifacts 2.18.2.1 16.01
compute metrics for evaluating of whole genome sequencing experiments 2.18.2.1 16.01
Downsample a file to retain a subset of the reads 2.18.2.1 16.01
assess sequence library complexity from read sequences 2.18.2.1 16.01
convert Fastq data into unaligned BAM 2.18.2.1 16.01
include or exclude aligned and unaligned reads and read lists 2.18.2.1 16.01
ensure that all mate-pair information is in sync between each read and it's mate pair 2.18.2.1 16.01
examine aligned records in BAM datasets to locate duplicate molecules 2.18.2.2 16.01
examine aligned records in BAM datasets to locate duplicate molecules 2.18.2.1 16.01
chart distribution of base qualities 2.18.2.1 16.01
merge alignment data with additional info stored in an unmapped BAM dataset 2.18.2.1 16.01
merges multiple SAM/BAM datasets into one 2.18.2.1 16.01
normalize fasta datasets 2.18.2.1 16.01
chart quality score distribution 2.18.2.1 16.01
reorder reads to match ordering in reference sequences 2.18.2.1 16.01
replace header in a SAM/BAM dataset 2.18.2.1 16.01
revert the original base qualities and add the mate cigar tag 2.18.2.1 16.01
revert SAM/BAM datasets to a previous state 2.18.2.1 16.01
extract reads and qualities from SAM/BAM dataset and convert to fastq 2.18.2.2 16.01
sort SAM/BAM dataset 2.18.2.1 16.01
assess validity of SAM/BAM dataset 2.18.2.1 16.01
compute metrics about datasets generated through hybrid-selection (e.g. exome) 2.18.2 16.01

Categories
SAM - Tools for manipulating alignments in the SAM format