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

BMC Bioinformatics

Table 4 Detected tandem repeats in bacterial test datasets

Sample	Seq. len. [bp]	Motif len. [bp]	Min. cov. (Eq. 5)	Unitigs				Scaffolds
				ABySS	Velvet	SPAdes	dnaasm	ABySS	Velvet	SPAdes	dnaasm
ERR351243	668	334	33	0	0	2	2	0	0	2	2
	371	16	371	0	0	0	0	0	0	0	0
SRR1981622	934	467	35	0	0	2	2	0	0	2	2
	706	307	39	0	0	0	0	0	0	0	0
	740	370	34	0	0	2	2	0	2	2	2
	1285	612	36	0	0	0	0	0	0	0	0
	1224	612	29	0	0	0	0	0	0	0	0
	1094	576	33	0	0	1.9	1.9	0	0	1.9	1.9
SRR1981619	934	467	35	0	0	2	2	0	0	2	2
	706	307	39	0	0	0	0	0	0	0	0
	740	370	34	0	0	2	2	0	0	2	2
	1285	612	36	0	0	0	0	0	0	0	0
	1224	612	29	0	0	0	0	0	0	0	0
	1094	576	33	0	0	1.9	1.9	0	0	1.9	1.9
SRR5431732	327	58	185	0	0	0	0	0	0	0	0
	335	69	160	0	0	0	0	0	0	0	0
	293	57	165	0	0	0	5.1	0	0	0	5.1
	267	51	164	0	0	0	5.2	0	0	0	5.2
	749	345	79	0	0	0	2.2	0	0	2.2	2.2
	579	111	186	0	0	0	5.2	0	0	0	5.2
	636	57	401	0	0	0	0	0	0	0	0

The numbers in the table depict number of motif repetitions in reconstructed DNA sequence. The proper restorations are in bold, the expected number of motif repetitions is defined as repetitive sequence length divided by the motif length. The table shows that only dnaasm and SPAdes reconstruct tandem repeats longer than insert size of paired-end tags in bacterial genomes. Moreover, dnaasm and SPAdes reconstruct these repetitive DNA regions even without using paired-end tags (unitigs). However, some of the tandem repeats are not reconstructed by any algorithm - they are contained in complex DNA regions, with many repeats of the same motif in other parts of the investigated genome

ISSN: 1471-2105