svim

Description

svim website

SVIM (pronounced SWIM) is a structural variant caller for long sequencing reads. It is able to detect and classify the following six classes of structural variation: deletions, insertions, inversions, tandem duplications, interspersed duplications and translocations. SVIM also estimates the genotypes of deletions, insertions, inversions and interspersed duplications. Unlike other methods, SVIM integrates information from across the genome to precisely distinguish similar events, such as tandem and interspersed duplications and simple insertions. In our experiments on simulated data and real datasets from PacBio and Nanopore sequencing machines, SVIM reached consistently better results than competing methods. Note! To analyze haploid or diploid genome assemblies or contigs, please use our other method SVIM-asm.

Environment Modules

Run module spider svim to find out what environment modules are available for this application.

Environment Variables

• HPC_SVIM_DIR - installation directory
• HPC_SVIM_BIN - executable directory

Citation

If you publish research that uses svim you have to cite it as follows:

Feel free to read and cite our paper in Bioinformatics: https://doi.org/10.1093/bioinformatics/btz041

Categories

biology