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

BMC Genomics

Table 1 Comparison of default and optimized CABOG assembly parameters

Default	Match	Relocation	Inversion	Redundancy	Coverage	Scaffold N50	Number of scaffolds
Arabidopsis thaliana	0.527	0.987	0.954	0.962	87.44%	117,128	57
Vitis vinifera	0.524	0.994	0.955	0.982	84.77%	114,280	60
Oryza sativa	0.535	0.992	0.966	0.982	88.49%	112,776	39
Populus trichocarpa	0.529	1.000	0.984	0.980	82.74%	134,082	65
Sorghum bicolor	0.542	0.889	0.944	0.956	86.58%	148,894	37
Zea mays	0.506	0.872	0.734	0.835	76.38%	52,719	140
Optimized	Match	Relocation	Inversion	Redundancy	Coverage	Scaffold N50	Number of scaffolds
Arabidopsis thaliana	0.645	0.996	0.996	0.979	99.86%	891,801	12
Vitis vinifera	0.694	0.993	0.953	0.992	99.46%	1,578,318	5
Oryza sativa	0.723	0.997	0.911	0.996	99.79%	1,785,140	6
Populus trichocarpa	0.813	1.000	1.000	0.997	99.16%	2,338,043	6
Sorghum bicolor	0.674	0.973	0.998	0.989	97.15%	663,137	11

Assembly evaluation scores and scaffold statistics determined for pseudomolecules created using 3 Mbp pools with 15x linear + 5x paired read coverage are shown for all of the genomes studied. Scores were determined using default and optimized assembly parameters, except for Z. mays that was only assembled using default parameters.

ISSN: 1471-2164