Results are shown in Fig 4 and S2 Table, where warmer colors indicate higher ploidy estimation accuracy .

When using the naive error model, ConPADE achieved substantially lower ploidy estimation accuracy , especially for coverages of 10X and 15X at intermediate ploidy levels (Fig 4 and S2 Table).

Because a coverage level of 50X resulted in correct estimated ploidies and high dosage estimation accuracy in the previous simulation sets, while still being viable in practice for de novo genome assembly efforts, we chose this value for more detailed simulations regarding contig lengths, the results of which are shown in Fig 5 and S5 Table.

Ploidy estimation accuracy for varying contig lengths and coverage levels.

This improvement was the result of: (i) some parameters being estimated accurately by the voltage-clamp protocol and (ii) information on two, rather than a single, state variable putting more constraints on the parameter values [36].

To improve parameter estimation accuracy , more improvement is typically gained from adding measurements of a different state variable than adding additional measurements of the same state variable [36].

Therefore, to improve the parameter estimation accuracy , we added a multi-step voltage clamp protocol to the objective function.