Table 1. Assembly statistics for both data sets, based on contigs with a minimal length of 500 bp. All program parameters are given in Table S9.

The lap and cgal likelihoods have been computed based on all reads mapping to any of the reference sequences. Ragout and MeDuSa depend on the quality of the initial assembly in terms of assembled sequence length; hence, we omit results for the Minia assembly here and refer to Table S10.

Strain	Assembly	No. of contigs	Total length (bp)	No of Ns	N50	LAP	CGAL
London	SPAdes	2555	3 792 691	0	1888	−11.01048	−6.90196e+08
	Minia	4183	2 631 422	0	930	−15.69016	−7.98656e+08
	SPAdes-Ragout	1	4 068 385	776 139	–	−12.52232	−4.8192e+08
	SPAdes-MeDuSa	77	4 333 801	1917	700 415	−7.97066	−5.00106e+08
	Minia-AGapEs	5	4 441,104	0 (313 628)	3 511 710	−7.26576	−3.55155e+08
Marseille	SPAdes	3201	6 072 375	0	4592	−11.03336	−6.0411e+08
	Minia	3089	3 636 663	0	1368	−15.05058	−8.71446e+08
	SPAdes-Ragout	2	4 564 323	542 013	4 530 296	−13.34526	−5.84186e+08
	SPAdes-MeDuSa	2155	6 052 372	618	1 643 585	−10.88342	−6.12532e+08
	Minia-AGapEs	6	4 350 872	0 (184 003)	3 459 919	−8.05526	−4.32647e+08