Accurate detection of tandem repeats from error-prone sequences with EquiRep

Table 2.

Performance on raw ONT long reads from C. elegans centromere

Read name/region Unit length EquiRep mTR TRF mreps TideHunter
SRR7594463.177832.regionA 26 0.9615 0.0385 0.0385 0.9615 0.7692
SRR7594463.177832.regionB 27 0.1111 0.1481 0.0000 0.9259 0.9259
SRR7594463.179860.regionA 27 0.9630 0.4074 4.9630 0.9630 4.8148
SRR7594463.179860.regionB 166 0.0904 0.0663 0.0783 0.9940 0.0904
SRR7594463.83311.regionA 166 0.0542 0.0241 0.0482 0.9940 0.0361
SRR7594463.83311.regionB 27 0.1481 0.6296 0.0741 0.9630 0.9259
SRR7594463.64356.regionA 226 0.0133 0.0044 0.0265 0.9956 0.0133
SRR7594463.64356.regionB 27 0.0741 0.1111 0.1111 0.9630 0.8148
SRR7594463.141714.regionB 27 0.5926 0.5185 0.5556 0.9630 3.1481
SRR7594463.82476.regionA 27 1.5556 0.5556 0.5556 0.9630 1.0741
SRR7594463.176233.regionA 27 0.8889 0.0741 0.2593 0.9630 0.8519
SRR7594463.176233.regionB 94 0.1596 0.1277 0.0745 0.9681 0.1383
SRR7594463.189890.regionB 94 0.4362 0.4149 0.8830 0.9894 0.4149
Average 0.4653 0.2400 0.5898 0.9690 1.0783
Count (<0.2) 7 8 8 0 4

  • Numbers are the normalized rotation-aware edit distance between the predicted units and the ground-truth unit. The averaged normalized rotation-aware edit distance and the number of instances in which a method achieves a rotation-aware edit distance less than 0.2 are summarized at the bottom.

This Article

  1. Published in Advance August 21, 2025, doi: 10.1101/gr.280750.125 Genome Res. 35: 2714-2721

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