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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: 29:1aac2a13842a
This revision can be installed: True
Times cloned / installed: 12541

Contents of this repository

Name Description Version Minimum Galaxy Version
revert SAM/BAM datasets to a previous state 2.18.2.1 16.01
revert the original base qualities and add the mate cigar tag 2.18.2.1 16.01
charts the GC bias metrics 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
perform SAM/BAM grooming 2.18.2.1 16.01
merge alignment data with additional info stored in an unmapped BAM dataset 2.18.2.1 16.01
sort SAM/BAM dataset 2.18.2.1 16.01
assess validity of SAM/BAM dataset 2.18.2.1 16.01
convert Fastq data into unaligned BAM 2.18.2.2 20.01
Downsample a file to retain a subset of the reads 2.18.2.1 16.01
chart distribution of base qualities 2.18.2.1 16.01
include or exclude aligned and unaligned reads and read lists 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
examine aligned records in BAM datasets to locate duplicate molecules 2.18.2.2 16.01
compute metrics about datasets generated through hybrid-selection (e.g. exome) 2.18.2 16.01
chart quality score distribution 2.18.2.1 16.01
plots distribution of insert sizes 2.18.2.1 16.01
add or replaces read group information 2.18.2.1 16.01
collect metrics about the alignment of RNA to various functional classes of loci in the genome 2.18.2.2 16.01
add comments to BAM dataset 2.18.2.1 16.01
examine aligned records in BAM datasets to locate duplicate molecules 2.18.2.3 16.01
reorder reads to match ordering in reference sequences 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
assess sequence library complexity from read sequences 2.18.2.1 16.01
convert coordinate data into picard interval list format 2.18.2.1 16.01
extract reads and qualities from SAM/BAM dataset and convert to fastq 2.18.2.2 16.01
charts the nucleotide distribution per cycle in a SAM or BAM dataset 2.18.2.1 16.01
writes a file containing summary alignment metrics 2.18.2.1 16.01
replace header in a SAM/BAM dataset 2.18.2.1 16.01

Categories
SAM - Tools for manipulating alignments in the SAM format