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Table 6 The efficiency of tandem repeats reconstruction from simulated data

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

Sequence len. [bp] Motif len. [bp] Min. cov. (Eq. 5) Unitigs Scaffolds
    ABySS Velvet SPAdes dnaasm ABySS Velvet SPAdes dnaasm
200 100 26 0/0/0 0/0/0 2/2/2 2/2/2 2/0/2 2/2/2 2/2/2 2/2/2
300 100 44 0/0/0 0/0/0 0/0/0 4/3/3 0/0/2 0/0/0 2/2/2 4/3/3
400 100 62 0/0/0 0/0/0 0/0/0 4/4/4 0/0/2 0/0/0 2/2/2 4/4/4
500 100 80 0/0/0 0/0/0 0/0/0 6/6/5 0/0/2 0/0/0 2/2/2 6/6/5
400 200 31 0/0/0 0/0/0 2/2/2 2/2/2 0/0/0 2/2/2 2/2/2 2/2/2
600 200 49 0/0/0 0/0/0 0/0/0 4/3/3 0/0/0 0/0/0 2/2/2 4/3/3
800 200 66 0/0/0 0/0/0 0/0/0 3/4/4 0/0/0 0/0/0 2/2/2 3/4/4
1000 200 84 0/0/0 0/0/0 0/0/0 6/6/5 0/0/0 0/0/0 2/2/2 6/6/5
600 300 32 0/0/0 0/0/0 2/2/2 2/2/2 0/0/0 0/0/0 2/2/2 2/2/2
900 300 50 0/0/0 0/0/0 0/0/0 3/3/3 0/0/0 0/0/0 2/2/2 3/3/3
1200 300 68 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 86 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 33 0/0/0 0/0/0 2/2/2 2/2/2 0/0/0 0/0/0 2/2/2 2/2/2
1200 400 51 0/0/0 0/0/0 0/0/0 3/3/3 0/0/0 0/0/0 0/0/0 3/3/3
1600 400 69 0/0/0 0/0/0 0/0/0 4/4/4 0/0/0 0/0/0 0/0/0 4/4/4
2000 400 87 0/0/0 0/0/0 0/0/0 5/5/5 0/0/0 0/0/0 0/0/0 5/5/5
1000 500 33 0/0/0 0/0/0 2/2/2 2/2/2 0/0/0 0/0/0 2/2/2 2/2/2
1500 500 51 0/0/0 0/0/0 0/0/0 3/3/3 0/0/0 0/0/0 0/0/0 3/3/3
2000 500 69 0/0/0 0/0/0 0/0/0 4/4/4 0/0/0 0/0/0 0/0/0 4/4/4
2500 500 87 0/0/0 0/0/0 0/0/0 5/5/5 0/0/0 0/0/0 0/0/0 5/5/5
  1. The numbers in the table depict number of motif repetitions in reconstructed DNA sequence for depth of coverage 50x, 100x and 150x, respectively. The proper restorations are in bold, the expected number of motif repetitions is defined as in Table 4. Only our algorithm was able to reconstruct tandem repeats with more than two motif repetition. It is worth paying attention to dnaasm results for 100 bp and 200 bp motifs, where increasing the depth of coverage increases the probability of tandem repeat correct reconstruction