This repo contains the scripts and vcf file data used to benchmark structural variation (SV) calling in Caenorhabditis elegans.
The SVE and FusorSV tools were used for shortread calling in BreakDancer, cnMOPS, CNVnator, Delly, fusorsv, Hydra, and Lumpy.
Longread calling was performed using Assemblytics, MUM&Co, pbsv, Sniffles, and SVIM.
The pipeline for simulated shortread data is here.
The pipeline for simulated longread data is here.
Data from the CeNDR project were used to compare the agreement between different SV callers.
The pipeline steps are explained here.
The longread with FusorSV pipeline is available here.
The shortread pipeline is available here.