cutesv
Long read based human genomic structural variation detection with cuteSV
smoove
structural variant calling and genotyping with existing tools, but, smoothly.
delly2
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
https://github.com/broadinstitute/gatk-sv
A structural variation pipeline for short-read sequencing
circle-map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
nrex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
https://github.com/brentp/bpbio
basepair bio: a single binary with many useful genomics subtools.
hmnfusion
A tool to aggregate results of fusion produced by Genefuse and Lumpy and calculate allelic frequency
https://github.com/brentp/duphold
don't get DUP'ed or DEL'ed by your putative SVs.
https://github.com/ampliconsuite/ecsimulator
Simulate ecDNA structures with user-specified properties.
sawfish
Joint structural variant and copy number variant caller for HiFi sequencing data
seabreeze
seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies - Published in JOSS (2025)
population-structural-var-calling-smoove
population structural variant calling with smoove