SHARC

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies. We provide packages to run on:

1. SLURM cluster
2. SGE cluster
3. Local
4. Singularity image
5. Docker image

https://github.com/UMCUGenetics/SHARC