GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
GRIDSS makes extensive use of the standard tags defined by SAM specifications. Due to the modular design, any step (such as split read identification) can be replaced by another implementation that also outputs using the standard tags. It is hoped that GRIDSS can serve as an exemplar modular structural variant pipeline designed for interoperability with other tools.
module spider gridss to find out what environment modules are available for this application.
- HPC_GRIDSS_DIR - installation directory
- HPC_GRIDSS_BIN - executable directory
If you publish research that uses gridss you have to cite it as follows:
Daniel L. Cameron, Jan Schröder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P. Speed and Anthony T. Papenfuss. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Research, 2017 doi: 10.1101/gr.222109.117