Table 1.

Evaluation of the simulated data (read length: 2× 250 bp). Low complexity data are 20 strains from 10 species, at average coverage 20× per strain. Medium complexity data are 100 strains from 30 species, at average coverage of 20× per strain. High complexity data are 1057 strains from 376 species, at average coverage of 10× per strain. XC is short for the species aware clustering that StrainXpress implements. Identity is the percentage of the completely matching bases of the contig in the optimal alignment with the ground truth. Error Rate = mismatch rate + indel rate

Assembly	Genome	Identity (%)	Total assembly	N50	NGA50	Misassembled	Error
	Fraction (%)		Length			Contig rate (%)	Rate (%)
Low complexity data (20×)
StrainXpress	93.45	99.93	99839190	2584	2955	0.11	0.06
SPAdes	74.74	99.91	58772582	5251	1749	0.09	0.04
GATB-Minia	73.33	99.78	67108819	6319	3240	0.25	0.09
IDBA-UD	62.73	99.91	54982071	9159	2381	0.04	0.09
MEGAHIT	62.69	99.71	55186304	20395	4356	1.05	0.15
metaSPAdes	66.56	99.76	62069880	18991	6723	0.10	0.11
Medium complexity data (20X)
StrainXpress	95.16	99.94	465118278	1685	2174	0.08	0.07
SPAdes	72.18	99.55	246604702	10966	2254	0.44	0.08
XC+SPAdes	59.05	99.63	206345396	4104	761	0.72	0.14
GATB-Minia	70.40	99.76	259945654	8324	3107	0.53	0.09
XC+GATB-Minia	70.55	99.77	267643882	8005	3305	0.61	0.11
IDBA-UD	62.01	99.81	216415403	5323	1059	0.22	0.08
XC+IDBA-UD	66.02	99.87	243646195	6107	1948	0.27	0.12
MEGAHIT	62.77	99.47	225937990	3400	1011	14.16	0.38
XC+MEGAHIT	68.77	99.63	267230659	13454	5483	1.06	0.24
metaSPAdes	63.38	99.81	228257504	19701	4394	0.37	0.14
XC+metaSPAdes	53.99	99.71	195286660	6394	729	0.78	0.24
High complexity data (10×)
StrainXpress	84.36	99.88	2278280614	1337	894	0.14	0.22
XC+MEGAHIT	75.63	99.56	2354992154	3358	1686	2.14	0.87
XC+IDBA-UD	70.18	99.68	2006623170	3540	1219	2.25	0.36
XC+GATB-Minia	68.20	99.78	1747199484	3382	794	1.07	0.25
XC+SPAdes	19.23	99.41	367171437	2542	-	3.16	0.64
XC+metaSPAdes	47.21	99.55	708596842	2613	-	1.46	0.45