GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

A tutorial on structural variant calling for short read sequencing data

Allele-specific copy number estimation with whole genome sequencing

scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis

GREMLIN: Genomic REarrangements by Machine Learning-based INspection

A QC pipeline for SVs calls based on coverage and SNP calls

Analysis and plotting functions for structural variant breakpoint data

Structural variant calling tutorial using long-reads.

Detection of inversions in P. falciparum from long read assemblies.

A human-first SV annotation snakemake pipeline based on nanotatoR working with optical mapping (Bionano Genomics) data

Quantify structural variants in clonal Daphnia genomes