Difference between revisions of "Svim-asm"
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Revision as of 17:15, 31 May 2022
Description
SVIM-asm (pronounced SWIM-assem) is a structural variant caller for haploid or diploid genome-genome alignments. It analyzes a given sorted BAM file (preferably from minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplications and inversions.
Note! To analyze raw long sequencing reads please use our other method SVIM.
Environment Modules
Run module spider svim-asm to find out what environment modules are available for this application.
System Variables
- HPC_SVIM-ASM_DIR - installation directory
- HPC_SVIM-ASM_BIN - executable directory
Citation
If you publish research that uses svim-asm you have to cite it as follows:
Feel free to read and cite our paper in Bioinformatics: https://doi.org/10.1093/bioinformatics/btaa1034