De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application

BMC Bioinformatics

Table 2 Evaluation of dnaasm in comparison to ABySS, Velvet and SPAdes assembler

Sample	Assembler	Type	No. of	N50 [bp]	Max [bp]	Avg.	Avg.
		of output	contigs			mis.	indels
ERR351243	ABySS	unitigs	79	40021	224368	0.00	1.61
	Velvet	unitigs	206	12813	38818	0.31	0.81
	SPAdes	unitigs	43	61281	287932	0.93	2.28
	dnaasm	unitigs	84	30628	191880	0.06	1.98
	ABySS	scaffolds	33	65136	224368	1.59	2.69
	Velvet	scaffolds	30	82451	224509	1.42	3.15
	SPAdes	scaffolds	27	74784	333212	1.23	2.53
	dnaasm	scaffolds	34	61265	333846	0.62	3.82
SRR1981622	ABySS	unitigs	81	36448	110990	1.11	0.99
	Velvet	unitigs	254	8636	27708	1.12	0.37
	SPAdes	unitigs	53	58976	228504	1.42	1.29
	dnaasm	unitigs	73	45793	134195	0.93	1.11
	ABySS	scaffolds	40	67391	207675	4.89	1.96
	Velvet	scaffolds	33	114376	285632	4.99	2.65
	SPAdes	scaffolds	35	98439	228504	3.26	2.09
	dnaasm	scaffolds	39	91627	228504	3.33	1.73
SRR1981619	ABySS	unitigs	80	36449	110993	8.36	2.85
	Velvet	unitigs	314	7163	22826	7.92	1.56
	SPAdes	unitigs	53	58765	228586	9.00	3.21
	dnaasm	unitigs	77	43959	134261	7.76	2.77
	ABySS	scaffolds	43	79578	111309	16.00	4.15
	Velvet	scaffolds	35	107026	492812	10.06	4.32
	SPAdes	scaffolds	34	98351	228586	8.99	4.31
	dnaasm	scaffolds	38	93136	256270	11.21	4.25
SRR5431732	ABySS	unitigs	559	11471	57586	17.85	2.90
	Velvet	unitigs	1032	4790	18304	17.98	2.57
	SPAdes	unitigs	238	30607	129385	21.02	3.74
	dnaasm	unitigs	416	16178	59383	21.68	4.10
	ABySS	scaffolds	208	35552	131767	19.81	4.51
	Velvet	scaffolds	202	41843	182297	21.99	7.21
	SPAdes	scaffolds	172	46834	159097	22.65	4.72
	dnaasm	scaffolds	354	19644	120052	25.13	4.42

Unitigs output depicts assembling mode without using paired-end tags, scaffolds - with paired reads. The table shows that the presented de novo assembler works comparatively in terms of the number of contigs, N50 statistic, the largest contig length and the quality (average number of mismatches and indels per 100000 aligned bases) of the resultant DNA sequences

ISSN: 1471-2105