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Table 1 Performance on simulated E. coli dataset

From: Kohdista: an efficient method to index and query possible Rmap alignments

MethodTime (s)Memory (MB)Align-mentsRecallPrecision
Kohdista2019.0907702/4305 (16%)702/771 (91%)
Kohdista (lax)37318.385453925/4305 (91%)3925/8545 (46%)
Valouev et al.1484.0742699/4305 (16%)699/742 (94%)
MalignerDP476.019591296/4305 (30%)1296/1959 (66%)
OMBlast11620781008806/4305 (19%)806/1008 (80%)
RefAligner3181.2992958/4305 (22%)948/992 (97%)
MalignerIX46.000/4305 (0%)0/0 (N/A)
OPTIMA45510756.500/4305 (0%)0/0 (N/A)
  1. Kohdista (lax) demonstrates that our indexing and search method is capable of finding the majority of ground truth alignments when the search is pruned to the more relaxed thresholds for chi-squared-cdf-thresh and binom-cdf-thresh, i.e., chi-squared-cdf-thresh = 0.02 and binom-cdf-thresh = 0.5