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Repository svdetect
Name: svdetect
Owner: bzeitouni
Synopsis: SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data
SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies
This tool aims to identifying structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.
More info at the SVDetect website: http://svdetect.sourceforge.net/

Setting up the galaxy version:
- set up the SAMtools directory location in all perl scripts (SAMTOOLS_BIN_DIR variable)
- set up the BEDtools directory location in the SVDetect_compare.pl perl script (BEDTOOLS_BIN_DIR variable)
- to use Circos via the circos_graph.xml file, make a symbolic link from your circos installation directory to the galaxy's svdetect location
>> ln -s /path/to/your/circos circos

Recommended PBS settings (in the "universe_wsgi.ini" file):
svdetect_preprocessing = pbs:///http/-l nodes=1:ppn=1,mem=4gb/
svdetect_run_parallel = pbs:///http/-l nodes=1:ppn=8,mem=50gb/
svdetect_compare = pbs:///http/-l nodes=1:ppn=1,mem=8gb/

22/01/2013 (rev28):
- release SVDetect r0.8b
- Import data script added
Type: unrestricted
Revision: 28:091714bd75a0
This revision can be installed: True
Times cloned / installed: 641

Contents of this repository

Name Description Version
and identify structural variants 1.0.0
BAM, chromosome info or sv files 1.0.0
structural variants between two samples 1.0.0
plots 1.1.0
to get abnormal pairs 1.0.0

Categories
Genomic Interval Operations - Tools for operating on genomic intervals
SAM - Tools for manipulating alignments in the SAM format
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis