| 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 |
hg clone https://toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| and identify structural variants | 1.0.0 | any | |
| BAM, chromosome info or sv files | 1.0.0 | any | |
| structural variants between two samples | 1.0.0 | any | |
| plots | 1.1.0 | any | |
| to get abnormal pairs | 1.0.0 | any | |