ProcaryaSV is a Snakemake pipeline to call SV, mainly CNVs from bacterial genomes. It employs 6 callers - DELLY2, LUMPY, Pindel, CNVnator,INSurVeyor, and CNproScan.
It provides two comparable outputs of merged SV - by ProcaryaSV's merging and by SURVIVOR's merge command. It starts with optional read trimming, reads alignment and then proceeds to CNV/SV calling.
All the sequencing reads and scripts are in the Onedrive folder here:
https://1drv.ms/f/s!Ah7xah3UhCitj4wk3LoPqk9C1OkdxQ?e=IyvG4j
The shared folder contains the "DATASETS_RUN" folder with both dataset, their configuration files, and bash scripts to run them. Just check the bash script and configuration file config.yaml for correct paths leading to FASTA references and ProcaryaSV pipeline folder.
ProcaryaSV manual can be found here or under Wiki tab above:
https://github.com/robinjugas/ProcaryaSV/wiki/ProcaryaSV-Manual
If you find some bugs, please fill the github bug report. I'll likely need example of the data to recreate the issue.