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

Table 5 The efficiency of tandem repeats reconstruction from simulated data

Sequence len. [bp]	Motif len. [bp]	Unitigs				Scaffolds
		ABySS	Velvet	SPAdes	dnaasm	ABySS	Velvet	SPAdes	dnaasm
200	100	0/0/0	0/0/0	2/2/2	2/2/2	2/2/2	2/2/2	2/2/2	2/2/2
300	100	0/0/0	0/0/0	0/0/0	3/3/3	2/3/3	0/2/0	2/2/2	3/3/3
400	100	0/0/0	0/0/0	0/0/0	4/4/4	2/4/4	0/0/0	2/2/2	4/4/4
500	100	0/0/0	0/0/0	0/0/0	5/5/6	2/0/5	0/0/0	2/2/2	5/5/6
400	200	0/0/0	0/0/0	2/2/2	2/2/2	0/2/2	2/2/2	2/2/2	2/2/2
600	200	0/0/0	0/0/0	0/0/0	3/3/3	0/0/0	0/2/2	2/2/2	3/3/3
800	200	0/0/0	0/0/0	0/0/0	4/4/4	0/0/0	0/0/2	2/2/2	4/4/4
1000	200	0/0/0	0/0/0	0/0/0	5/5/6	0/0/0	0/0/0	2/2/2	5/5/6
600	300	0/0/0	0/0/0	2/2/2	2/2/2	0/2/2	0/2/2	2/2/2	2/2/2
900	300	0/0/0	0/0/0	0/0/0	3/3/3	0/0/2	0/0/2	2/2/2	3/3/3
1200	300	0/0/0	0/0/0	0/0/0	4/4/4	0/0/0	0/0/0	2/2/2	4/4/4
1500	300	0/0/0	0/0/0	0/0/0	5/5/5	0/0/0	0/0/0	2/2/2	5/5/5
800	400	0/0/0	0/0/0	2/2/2	2/2/2	0/2/0	0/2/2	2/2/2	2/2/2
1200	400	0/0/0	0/0/0	0/0/0	3/3/3	0/2/0	0/0/0	0/2/2	3/3/3
1600	400	0/0/0	0/0/0	0/0/0	4/4/4	0/2/0	0/0/0	0/2/2	4/4/4
2000	400	0/0/0	0/0/0	0/0/0	5/5/5	0/0/0	0/0/0	0/2/2	5/5/5
1000	500	0/0/0	0/0/0	2/2/2	2/2/2	0/2/2	0/2/2	2/2/2	2/2/2
1500	500	0/0/0	0/0/0	0/0/0	3/3/3	0/2/0	0/0/0	0/2/2	3/3/3
2000	500	0/0/0	0/0/0	0/0/0	4/4/4	0/2/0	0/0/0	0/2/2	4/4/4
2500	500	0/0/0	0/0/0	0/0/0	5/5/5	0/0/0	0/0/0	0/2/2	5/5/5

The numbers in the table depict number of motif repetitions in reconstructed DNA sequence for insert size mean equal to 250 bp, 750 bp and 1250 bp, respectively. The proper restorations are in bold, the expected number of motif repetitions is defined as in Table 4. Only dnaasm was able to reconstruct tandem repeats with more than two motif repetition from unitigs. Additionally, the ABySS results of 100 bp motif reconstruction from paired-end tags shows, that increasing the insert size value increases the probability of tandem repeat reconstruction