Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

BMC Genomics

Table 3 Pooled BAC assembly scores for five genomes

Species	Pool Size	Match	Relocation	Inversion	Redundancy	Coverage	Scaffold N50	Number of scaffolds
A. thaliana	3M	0.527	0.994	0.954	0.962	87.44%	117,128	57
A. thaliana	6M	0.518	0.997	0.976	0.969	86.55%	126,619	100
A. thaliana	9M	0.511	0.927	0.985	0.975	85.72%	121,006	144
A. thaliana	12M	0.510	0.999	0.981	0.982	87.36%	147,618	152
V. vinifera	3M	0.524	0.997	0.955	0.988	84.76%	114,280	60
V. vinifera	6M	0.511	0.997	0.974	0.972	80.60%	113,117	143
V. vinifera	9M	0.510	0.997	0.953	0.969	82.96%	116,543	173
V. vinifera	12M	0.507	0.994	0.941	0.973	82.48%	115,403	226
O. sativa	3M	0.535	0.996	0.966	0.989	88.45%	112,776	39
O. sativa	6M	0.519	0.983	0.895	0.983	87.10%	140,891	90
O. sativa	9M	0.508	0.961	0.902	0.977	84.91%	117,728	141
O. sativa	12M	0.507	0.958	0.869	0.979	84.72%	114,523	219
P. trichocarpa	3M	0.529	1.000	0.984	0.981	82.68%	134,082	65
P. trichocarpa	6M	0.513	1.000	0.980	0.992	82.31%	119,756	114
P. trichocarpa	9M	0.508	1.000	0.995	0.992	81.39%	124,798	182
P. trichocarpa	12M	0.506	1.000	0.979	0.989	80.99%	117,268	256
S. bicolor	3M	0.542	0.945	0.944	0.957	86.56%	148,894	37
S. bicolor	6M	0.520	0.889	0.939	0.955	86.03%	147,854	81
S. bicolor	9M	0.508	0.922	0.898	0.953	84.59%	112,136	213
S. bicolor	12M	0.504	0.905	0.859	0.953	83.57%	96,480	274
Z. mays	3M	0.506	0.872	0.734	0.835	76.38%	52,719	140
Z. mays	6M	0.503	0.857	0.679	0.832	79.31%	40,526	320
Z. mays	9M	0.502	0.847	0.687	0.820	80.33%	37,394	485
Z. mays	12M	0.501	0.855	0.674	0.815	82.39%	37,122	577

Evaluation scores and scaffold statistics for assemblies determined using 15x linear + 5x paired read coverage and pool sizes 3 Mbp, 6 Mbp, 9 Mbp, and 12 Mbp are shown for all of the genomes studied. Default assembly parameters were used.

ISSN: 1471-2164