Table 1. Genome and assembly statistics.

		No. of scaffolds	N50	N90	Ns	Longest scaffold	Size [%]
C. parapsilosis	ref	9	2 091 826	957 321	0	3 023 470	-
SPAdes	min	188	2607	111	0	35 992	102.61
	max	3861	183 185	38 399	469 611	975 662	199.59
dipSPAdes	min	47	140 841	10 876	0	369 644	44.06
	max	201	443 228	168 647	0	1 277 709	100.67
Platanus	min	97	8525	2240	7816	62 024	99.30
	max	3503	314 901	105 072	115 364	1 233 366	156.29
Redundansa	min	16	294 087	88 621	277	870 098	99.58
	max	109	1 880 160	557 645	73 286	3 104 871	106.17
Redundansb	min	13	432 772	179 116	3053	1 026 161	99.39
	max	49	1 599 252	651 286	38 113	3 144 038	100.35
A. thaliana	ref	5	23 459 830	18 585 056	185 738	30 427 671	–
SPAdes	min	7261	1242	111	0	14 802	84.00
	max	45 769	91 641	6562	0	786 328	190.87
dipSPAdes	min	978	38 818	4393	0	378 250	57.99
	max	4305	217 604	41 794	0	1 120 742	81.89
Platanus	min	1225	9078	2304	300 250	89 082	96.80
	max	29 856	330 677	63 136	1 907 392	2 741 383	152.32
Redundansa	min	127	810 991	51 721	191 751	2 162 015	92.30
	max	1471	2 909 961	612 329	1 830 833	9 950 963	101.68
Redundansb	min	97	1 796 239	163 909	151 424	7 206 143	97.67
	max	864	13 602 130	4 371 075	1 162 308	28 354 754	101.29

All genomes used in this study are listed. For respective reference genomes, we provide it's accession together with number of scaffolds/chromosomes, N50 and N90, cumulative size of gaps and the length of the longest scaffold / chromosome. For assemblies produced in this study based on simulated heterozygous genomes with various level of divergence between heterozygous regions (1–40%) and level of loss of heterozygosity (0–100%), we provide minimum and maximum value for each of these metrics obtained. In addition, minimum and maximum percentage of expected assembly size is given.

^aRedundans reconstruction started with SPAdes contigs.

^bRedundans reconstruction started with Platanus scaffolds.