Pipeline for detecting DNA inversions in sequencing data

This pipeline's purpose is to use Whole Genome Sequencing (WGS) data in order to detect genomic inversions in the genomes of bacteria and calculate their prevalence in the population. It is  a supplementary material to the paper "Systematic Identification and Quantification of Phase Variation in Commensal and Pathogenic E.coli" (Goldberg, A. et al., Genome Medicine 2014). A step-by-step guide instructs how to find and quantify inversions.

Download zip file with instructions, Matlab code and article.