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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
Type: unrestricted
Revision: 33:3f254c5ced1d
This revision can be installed: True
Times cloned / installed: 18097

Contents of this repository

Name Description Version Minimum Galaxy Version
revert SAM/BAM datasets to a previous state 22.05
revert the original base qualities and add the mate cigar tag 22.05
charts the GC bias metrics 22.05
Collect metrics to quantify single-base sequencing artifacts 22.05
compute metrics for evaluating of whole genome sequencing experiments 22.05
perform SAM/BAM grooming 22.05
merge alignment data with additional info stored in an unmapped BAM dataset 22.05
sort SAM/BAM dataset 22.05
assess validity of SAM/BAM dataset 22.05
convert Fastq data into unaligned BAM 22.05
Downsample a file to retain a subset of the reads 22.05
chart distribution of base qualities 22.05
include or exclude aligned and unaligned reads and read lists 22.05
merges multiple SAM/BAM datasets into one 22.05
normalize fasta datasets 22.05
examine aligned records in BAM datasets to locate duplicate molecules 22.05
compute metrics about datasets generated through hybrid-selection (e.g. exome) 3.1.1 22.05
chart quality score distribution 22.05
plots distribution of insert sizes 22.05
add or replaces read group information 22.05
collect metrics about the alignment of RNA to various functional classes of loci in the genome 22.05
add comments to BAM dataset 22.05
examine aligned records in BAM datasets to locate duplicate molecules 22.05
reorder reads to match ordering in reference sequences 22.05
ensure that all mate-pair information is in sync between each read and it's mate pair 22.05
assess sequence library complexity from read sequences 22.05
convert coordinate data into picard interval list format 22.05
extract reads and qualities from SAM/BAM dataset and convert to fastq 22.05
charts the nucleotide distribution per cycle in a SAM or BAM dataset 22.05
writes a file containing summary alignment metrics 22.05
replace header in a SAM/BAM dataset 22.05

SAM - Tools for manipulating alignments in the SAM format