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

BMC Genomics

Table 5 Zea mays assembly scroes for a single insert size library versus multiple insert size libraries

Coverage	Pool Size	Match	Relocation	Inversion	Redundancy	Coverage	Scaffold N50	Number of scaffolds
15L + 5P (3kb)	3M	0.506	0.872	0.734	0.835	76.38%	52,719	140
15L + 5P (3kb)	6M	0.503	0.857	0.679	0.832	79.31%	40,526	320
15L + 5P (3kb)	9M	0.502	0.847	0.687	0.820	80.33%	37,394	485
15L + 5P (3kb)	12M	0.501	0.855	0.674	0.815	82.39%	37,122	577
15L + 2.5P (3kb) + 2.5P (8 kb)	3M	0.511	0.717	0.728	0.818	85.83%	104,440	94
15L + 2.5P (3kb) + 2.5P (8kb)	6M	0.504	0.700	0.733	0.799	84.25%	104,094	216
15L + 2.5P (3 kb) + 2.5P (8 kb)	9M	0.503	0.752	0.703	0.807	85.54%	76,589	337
15L + 2.5P (3kb) + 2.5P (8kb)	12M	0.502	0.815	0.717	0.778	86.36%	69,622	432

Assembly evaluation scores and scaffold statistics are shown for maize 3--12 Mbp pool assemblies constructed from (i) 15X linear + 5X paired 3 Kbp insert size library reads, and (ii) 15X linear + 2.5X paired 3 Kbp insert size library + 2.5X paired 8 Kbp insert size library reads.

ISSN: 1471-2164