Fig. 1

Workflow of data recombination and coverage analysis. Blue rectangles represent the methods used; yellow squares represent the output files. Lozenges represent name labels for the tools used. a Galocal, a pipeline for analyzing sequencing data and calculating depth of coverage. This pipeline encompasses a list of tools to analyze paired-end Illumina sequence. It allows (1) reads’ mapping, (2) filter and remove duplicates, (3) call variant and (4) calculate per base depth of coverage. At the end of this step, three text files are generated (.vcf, .doc and .bam). b UGDR, a pipeline to analyze recombination. This pipeline considers two VCF files as an input (one file for the Parental or reference strain P.vcf and a file for the potentially recombined strain R.vcf). (1) The pipeline calculates the ratio from the VCF files and classify them according to their origins: Parental/reference alleles file and Recombined alleles file (2) Compare the allele ratio between parent/reference and the recombined strains, univariate ratios are written in the invariant alleles file and the varying ratios are written in variant alleles file. (3) The last step is to compare the alleles ratios and stock the result in Region of recombination file. Once the files are created, recombination profile is created. c NDoC, a pipeline to calculate Depth of Coverage. A depth of coverage is calculated within a 1 kb window from the parental and the recombined DOC files and the results are written in two distinct files. Next, the normalized depth of coverage is calculated, and the data are stoked in xx_normalized1KB file (xx: name of the potentially recombined strains). Lastly the coverage plot per chromosome is plotted