Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

Table 2 Merqury quality and completeness statistics for Arabidopsis thaliana and human genome assemblies

	Assembly	Continuity (Mb)				QV			k-mer completeness (%)				BUSCO (%)
	Assembly	Total	# Contigs	Max	NG50	Meryl	Mash	Map	All	Hap1	Hap2	PPV	Comp.	Dup.	Frag.	Mis.
*A. thaliana* Col x Cvi F1	TrioCanu
	Col	124	215	13.1	4.6	35.1	34.6	37.5	83.8	99.5	0.7	99.3	98.2	1.6	0.5	1.3
	Cvi	122	163	12.2	5.6	36.4	35.9	38.6	83.6	1.1	99.4	98.9	98.0	1.4	0.4	1.6
	Col + Cvi	246	378	13.1	5.5	35.7	33.0	38.0	98.3	99.7	99.4	99.1	98.2	78.8	0.2	1.6
	FALCON-Unzip
	pri	140	172	13.3	8.0	34.8	33.9	36.9	87.1	65.2	59.8	N/A	98.1	6.2	0.3	1.6
	alt	105	248	11.6	4.3	38.3	37.9	39.9	74.5	38.2	40.6	N/A	93.1	2.0	0.3	6.6
	pri + alt	245	420	13.3	6.9	36.0	33.5	37.9	97.8	99.1	98.2	N/A	98.1	93.2	0.3	1.6
	Canu	248	2368	6.9	2.3	29.3	26.8	27.2	95.7	90.5	90.8	N/A	97.6	61.5	0.4	2.0
*H. sapiens* NA12878	TrioCanu
	mat	2749	7388	9.0	1.1	31.3	30.4	34.1	94.0	90.7	0.9	99.1	86.5	0.8	6.9	6.6
	pat	2743	7252	11.5	1.1	31.0	30.1	34.1	93.7	1.0	91.0	98.8	85.1	0.7	7.8	7.1
	mat + pat	5492	14,640	11.5	1.1	31.1	27.5	34.1	98.2	90.9	91.2	99.0	90.0	47.3	5.0	5.0

All bases in the continuity stats are in Mbp. Haploid genome size of 130 Mbp and 3.2 Gbp was used for NG50 in the A. thaliana and H. sapiens NA12878 haploid assemblies, respectively, with twice the haploid genome size for combined assemblies. Merqury-specific column headers are in bold, including k-mer-based quality (QV) and completeness estimates. Merqury includes both exact (Meryl) and approximate (Mash) methods for measuring k-mer QV, while completeness uses only the exact k-mer counting method. Consensus QV scores are Phred-scaled where QV = − 10 log₁₀ E for a probability of error E at each base in the assembly. K-mer completeness is measured by the fraction of all distinct, reliable k-mers (all) and haplotype specific k-mers. Hap1 and Hap2 correspond to Col and Cvi in A. thaliana, maternal and paternal in NA12878. BUSCO v3 was run with embryophyta_odb9 (n = 1440) for A. thaliana and mammalia_odb9 (n = 4104) for NA12878
Map. mapping, Comp. complete, Dup. duplicated, Frag. fragmented, Mis. missing

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