Fig. 2.—

The SEX-DETector pipeline: from required data to outputs. The advised number of offspring individual to sequence was determined with simulations. Parameters of the model are written in red: the segregation type π, the parents true genotype frequencies α and β, the genotyping error ϵ and the Y genotyping error p. An X/Y system is represented here but the pipeline is equivalent for a Z/W system. For a U/V system, only two individuals of each sex and one parent are advised and can be sequenced on a single Illumina Hi-seq 2000 lane. The pipeline was implemented in Galaxy for steps following Trinity. Note that different assembler and mapper could be chosen, only the genotyper Reads2snp is required to run SEX-DETector.