The work flow for multiple chromosomes. Work flow for multiple (G') chromosomes. (a) IRiS pipeline: In Phase 1, we use two different parameter settings to obtain an intermediate matrix (called recomatrix) for Phase 2. The second phase constructs the ARG. (b) Some Z' ≤ G' chromosomes are used through the IRiS pipeline and the Z' results are consolidated to obtain the final analysis. (c) The IRiS pipeline is used on an ensemble sequence (see Fig. 2) of the G' chromosomes some N times and the results are consolidated.