svim-asm¶

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.

Environment Variables¶

HPC_SVIMASM_DIR - installation directory
HPC_SVIMASM_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

Categories¶

biology