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Run your first simulation
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Success criteria
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§9.1 met
Coverage
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every locus cut
Type-3 gaps filled
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of genome · target ≥ 1%
Mean assembly size
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molecules per complex
Does the mechanism work?
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Long assemblies formfinal mean assembly size > 2
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Internal junctions beat free endsterminus fraction < gap fraction
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External material wedged intype-3 gaps filled to a few % of the genome
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Coverage (§2.3): run to compute.
Assembly size across the cooling schedule
§12.1Mean assembly size and number of assemblies as the pool cools from hot to cold.
Gap-size distribution
§12.2Final census point, uncapped widths g1…g_over. Narrow gaps are the productive ones.
Growth per cycle
§12.4Total nucleotides across cycles. Rising = the pool is copying itself. Needs cycles > 1.