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Table 4 Detected tandem repeats in bacterial test datasets

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

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
  1. 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