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

BMC Bioinformatics

Table 3 Evaluation of tandem repeats reconstruction algorithm in dnaasm

Sample	Type of output	With tandem repeats reconstruction			Without tandem repeats reconstruction
		No. of contigs	N50 [bp]	Max [bp]	No. of contigs	N50 [bp]	Max [bp]
ERR351243	unitigs	84	30628	191880	93	27268	176501
	scaffolds	34	61265	333846	34	61265	333846
SRR1981622	unitigs	73	45793	134195	82	33787	110992
	scaffolds	39	91627	228504	43	80288	206366
SRR1981619	unitigs	77	43959	134261	81	36452	110995
	scaffolds	38	93136	256270	42	84434	205320
SRR5431732	unitigs	416	16178	59383	450	14774	47710
	scaffolds	354	19644	120052	388	17344	120052

Unitigs output depicts assembling mode without using paired-end tags, scaffolds - with paired reads. The table shows that tandem repeats reconstructuion process could significantly improve the results in terms of the number of contigs, N50 statistic and the largest contig length

ISSN: 1471-2105