mikischikora/persvade repository overview

perSVade: personalized Structural Variation detection

perSVade runs structural variation (SV), small variant (SNPs and IN/DELs) and read depth-based Copy Number Variation (CNV) calling and annotation from paired-end short reads. Everything with a single bash command.

The SV calling pipeline finds breakpoints with GRIDSS (https://github.com/PapenfussLab/gridss⁠) and summarizes them into complex structural variants with CLOVE (https://github.com/PapenfussLab/clove⁠), with some added features. perSVade provides an automated benchmarking and parameter selection for these methods in any genome or sequencing run. This is useful for species without recommended running and filtering parameters. In addition, it provides an automated report of the SV calling accuracy on simulations and real data, useful to assess the confidence of the results.

The code and documentation can be found in https://github.com/Gabaldonlab/perSVade⁠. Note that the 'releases' from this github repository are equivalent to the 'tag' from dockerhub. You may check in github the changes that occurred between versions.