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

BMC Genomics

Table 4 Scores for Arabidopsis assemblies determined using the pooled BAC and WGS strategies

	Size (Mbp)	Method	Match	Relocation	Inversion	Redundancy	Coverage	Scaffold N50	Number of scaffolds
chr1	30.4	WGS	0.501	0.986	0.957	0.891	90.42%
chr2	19.7	WGS	0.496	0.940	0.954	0.846	84.97%
chr3	23.5	WGS	0.503	0.988	0.939	0.893	90.09%	207,281	3,268
chr4	18.6	WGS	0.479	0.992	0.950	0.778	76.01%
chr5	30.0	WGS	0.492	0.993	0.955	0.804	83.02%
chr1	30.4	Pooled	0.512	1.000	0.968	0.979	94.11%	369,269	497
chr2	19.7	Pooled	0.518	0.998	0.962	0.982	96.01%	534,038	291
chr3	23.5	Pooled	0.515	0.998	0.953	0.978	97.23%	464,102	431
chr4	18.6	Pooled	0.518	0.999	0.955	0.977	93.43%	355,538	370
chr5	30.0	Pooled	0.537	1.000	0.967	0.978	96.36%	750,202	390

Assembly evaluation scores and scaffold statistics are shown for the Arabidopsis chromosome pseudomolecules obtained from assembling WGS and pooled BAC data. Chromosome scaffold statistics for pooled assemblies are averages over the values for each pool in that chromosome. Optimized assembly parameters were used.

ISSN: 1471-2164