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Table 5 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] 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
  1. 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