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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: 22:f6ced08779c4
This revision can be installed: True
Times cloned / installed: 18070

Contents of this repository

Name Description Version Minimum Galaxy Version
convert coordinate data into picard interval list format 2.18.2.1 16.01
assess validity of SAM/BAM dataset 2.18.2.1 16.01
convert Fastq data into unaligned BAM 2.18.2.1 16.01
collect metrics about the alignment of RNA to various functional classes of loci in the genome 2.18.2.1 16.01
Downsample a file to retain a subset of the reads 2.18.2.1 16.01
chart quality score distribution 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
sort SAM/BAM dataset 2.18.2.1 16.01
compute metrics for evaluating of whole genome sequencing experiments 2.18.2.1 16.01
charts the nucleotide distribution per cycle in a SAM or BAM dataset 2.18.2.1 16.01
chart distribution of base qualities 2.18.2.1 16.01
charts the GC bias metrics 2.18.2.1 16.01
merges multiple SAM/BAM datasets into one 2.18.2.1 16.01
plots distribution of insert sizes 2.18.2.1 16.01
merge alignment data with additional info stored in an unmapped BAM dataset 2.18.2.1 16.01
perform SAM/BAM grooming 2.18.2.1 16.01
assess sequence library complexity from read sequences 2.18.2.1 16.01
examine aligned records in BAM datasets to locate duplicate molecules 2.18.2.1 16.01
examine aligned records in BAM datasets to locate duplicate molecules 2.18.2.1 16.01
add or replaces read group information 2.18.2.1 16.01
add comments to BAM dataset 2.18.2.1 16.01
extract reads and qualities from SAM/BAM dataset and convert to fastq 2.18.2.1 16.01
normalize fasta datasets 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
include or exclude aligned and unaligned reads and read lists 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
writes a file containing summary alignment metrics 2.18.2.1 16.01

Categories
SAM - Tools for manipulating alignments in the SAM format