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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: 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 16.01
revert the original base qualities and add the mate cigar tag 16.01
charts the GC bias metrics 16.01
Collect metrics to quantify single-base sequencing artifacts 16.01
compute metrics for evaluating of whole genome sequencing experiments 16.01
perform SAM/BAM grooming 16.01
merge alignment data with additional info stored in an unmapped BAM dataset 16.01
sort SAM/BAM dataset 16.01
assess validity of SAM/BAM dataset 16.01
convert Fastq data into unaligned BAM 20.01
Downsample a file to retain a subset of the reads 16.01
chart distribution of base qualities 16.01
include or exclude aligned and unaligned reads and read lists 16.01
merges multiple SAM/BAM datasets into one 16.01
normalize fasta datasets 16.01
examine aligned records in BAM datasets to locate duplicate molecules 16.01
compute metrics about datasets generated through hybrid-selection (e.g. exome) 2.18.2 16.01
chart quality score distribution 16.01
plots distribution of insert sizes 16.01
add or replaces read group information 16.01
collect metrics about the alignment of RNA to various functional classes of loci in the genome 16.01
add comments to BAM dataset 16.01
examine aligned records in BAM datasets to locate duplicate molecules 16.01
reorder reads to match ordering in reference sequences 16.01
ensure that all mate-pair information is in sync between each read and it's mate pair 16.01
assess sequence library complexity from read sequences 16.01
convert coordinate data into picard interval list format 16.01
extract reads and qualities from SAM/BAM dataset and convert to fastq 16.01
charts the nucleotide distribution per cycle in a SAM or BAM dataset 16.01
writes a file containing summary alignment metrics 16.01
replace header in a SAM/BAM dataset 16.01

SAM - Tools for manipulating alignments in the SAM format