Table 2. Metrics for LACHESIS-based scaffolding of simulated assemblies.

Simulated assemblies were created by breaking up the human reference genome into simulated contigs of varying sizes, and then using LACHESIS to cluster, order and orient the simulated contigs. The simulated contigs’ expected order and orientation are derived from their true position in the reference genome. Ordering and orientation errors are defined as in Table 1.

Metric	Simulated contig size
	10 Kb	20 Kb	50 Kb	100 Kb	200 Kb	500 Kb	1 Mb
Number of contigs	309,579	154,794	61,927	30,970	15,489	6,206	3,113
% sequence clustered into groups	30.1%	74.2%	91.9%	92.7%	92.9%	93.1%	93.4%
% clustered sequence mis-clustered	1.6%	0.47%	0.41%	0.46%	0.66%	0.66%	0.26%
% clustered sequence ordered	48.5%	79.9%	98.9%	99.8%	99.97%	99.93%	99.98%
% ordered sequence w/ ordering errors	37.2%	18.0%	4.4%	2.2%	1.4%	0.8%	0.8%
% ordered sequence w/ orientation errors	44.8%	28.7%	7.7%	2.6%	1.2%	0.8%	0.7%