Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data

The repository for codes developed to generated the Maize NC358 assemblies and analyses.

Bionano SCaffolding Correction Tool

an open-source (GPLv3) standalone Python package to analyze optical mapping data, with de novo repeat motif detection and analysis capabilities

Thesis results

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

bionano annovar annotation

A combination of optical genome mapping with Bionano and whole genome sequencing short-read data. This pipeline was created to help integrate structural variant calling from these two technologies.