Ensemble analysis of adaptive compressed genome sequencing strategies

BMC Bioinformatics

Table 5 Effect of threshold τ .

p/5	τ	E[t] (Gbps)	P= (q0000, q1000, q0100, q1100, q0010, q1010, q0110, q1110, q0001, q1001, q0101, q1101, q0011, q1011, q0111, q1111 )
(1, 1, 2, 4)	0	1.428	(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1)
(1, 1, 2, 4)	0.1	1.423	(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1)
(1, 1, 2, 4)	0.2	1.407	(0, 0, 0, 0, 0, 0, 0, 0.0123, 0, 0, 0, 0.0001, 0, 0, 0, 0.9876)
(1, 1, 2, 4)	0.4	1.266	(0, 0, 0, 0.0002, 0, 0, 0.0008, 0.0411, 0, 0, ∈, 0.0794, 0, 0, 0.1621, 0.7165)
(1, 1, 1, 5)	0	1.418	(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1)
(1, 1, 1, 5)	0.1	1.414	(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1)
(1, 1, 1, 5)	0.2	1.383	(0, 0, 0, 0, 0, 0, 0, 0.0020, 0, 0, 0, 0.0271, 0, 0, 0, 0.9709)
(1, 1, 1, 5)	0.4	1.214	(0, 0, 0, 0.0013, 0, 0, ∈, 0.0078, 0, 0, ∈, 0.2308, 0, 0, 0.1369, 0.6231)

The genome sizes are (4, 12, 2, 1) Mbps and the total number of cells is n = 40. qI for I ∈ {0, 1}^s is the joint probability of capturing distinct genome j if I_j = 1 and missing it if Ij = 0 for j = 1, 2, . . . , s. Different values of I are explicitly given as binary strings in the fourth column. ∈ is a non-zero probability less than 10⁻⁴.

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