A highly accurate heuristic algorithm for the haplotype assembly problem

BMC Genomics

Table 3 Comparisons of the algorithms when l = 350.

e	c	SpeedHap	Fast Hare	2d-mec	HapCUT	MLF	SHR-three	DGS	Ours
0.0	3	0.999	0.990	0.965	1.000	0.864	0.830	0.999	1.000
	5	1.000	0.999	0.993	1.000	0.929	0.829	1.000	1.000
	8	1.000	1.000	0.998	1.000	0.969	0.895	1.000	1.000
	10	1.000	0.999	0.999	1.000	0.981	0.878	1.000	1.000
0.1	3	0.819	0.871	0.837	0.930	0.752	0.682	0.926	0.970
	5	0.959	0.945	0.913	0.913	0.858	0.724	0.978	0.993
	8	0.984	0.985	0.964	0.896	0.933	0.742	0.996	0.999
	10	0.984	0.995	0.978	0.888	0.962	0.728	0.998	1.000
0.2	3	0.439	0.684	0.675	0.771	0.642	0.591	0.691	0.877
	5	0.729	0.746	0.728	0.831	0.728	0.632	0.769	0.953
	8	0.825	0.853	0.791	0.862	0.798	0.670	0.842	0.988
	10	0.855	0.877	0.817	0.867	0.831	0.668	0.878	0.994
0.3	3	0.251	0.590	0.593	0.565	0.581	0.548	0.578	0.725
	5	0.578	0.602	0.606	0.582	0.606	0.557	0.609	0.833
	8	0.629	0.626	0.623	0.621	0.634	0.604	0.628	0.922
	10	0.638	0.644	0.634	0.664	0.641	0.619	0.641	0.951

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