A highly accurate heuristic algorithm for the haplotype assembly problem

BMC Genomics

Table 4 Comparisons of the algorithms when l = 700.

e	c	SpeedHap	Fast Hare	2d-mec	HapCUT	MLF	SHR-three	DGS	Ours
0.0	3	0.999	0.988	0.946	1.000	0.787	0.781	0.999	0.997
	5	1.000	0.999	0.976	1.000	0.854	0.832	1.000	0.999
	8	1.000	1.000	0.992	1.000	0.919	0.868	1.000	1.000
	10	1.000	0.999	0.997	1.000	0.933	0.898	1.000	1.000
0.1	3	0.705	0.829	0.786	0.927	0.698	0.668	0.931	0.951
	5	0.947	0.949	0.880	0.916	0.809	0.716	0.977	0.989
	8	0.985	0.986	0.948	0.896	0.863	0.743	0.987	0.997
	10	0.986	0.995	0.965	0.889	0.884	0.726	0.997	0.998
0.2	3	0.199	0.652	0.647	0.753	0.624	0.591	0.669	0.837
	5	0.681	0.712	0.697	0.825	0.682	0.617	0.741	0.927
	8	0.801	0.808	0.751	0.856	0.747	0.653	0.818	0.974
	10	0.813	0.872	0.778	0.861	0.765	0.675	0.861	0.982
0.3	3	0.095	0.581	0.583	0.552	0.570	0.536	0.573	0.676
	5	0.523	0.591	0.596	0.555	0.594	0.562	0.595	0.777
	8	0.616	0.615	0.613	0.597	0.614	0.611	0.614	0.876
	10	0.627	0.616	0.622	0.645	0.625	0.625	0.622	0.909

The columns e and c refer to the error rate and coverage rate, respectively. Columns 3-9 represent the reconstruction rate of the seven algorithms, i.e. SpeedHap, Fast Hare, 2d-mec, HapCUT, MLF, SHR-three and DGS. For each combination of e and c, the best among the seven algorithms is highlighted in bold. The last column lists the reconstruction rate of our algorithm.

ISSN: 1471-2164