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Table 2 Assembly results for E. coli Rmap data simulated by OMSim using enzyme BspQI

From: Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph

Assembler Run time Peak Memory No. of contigs Max Mean GF(%) MA
Valouev 8.5 d 0.48 5 102 (1.0 Mbp) 56 (0.5 Mbp) 48 0
Solve 48.1 h 1.18 1 631 (4.9 Mbp) 631 (4.9 Mbp) 100 0
\({\textsc {rmapper}}\) 6 m 0.46 2 529 (4.6 Mbp) 526 (4.5 Mbp) 100 0
  1. The dataset has 23,450 Rmaps of mean size of 42 fragments and coverage of 900x. The peak memory is given in gigabytes (GB). The run time is reported in second (s) minutes (m), hours (h) and days (d). rmapperwas run with \(k=6\), \(D={15000}\) and error tolerance parameter setting \(t_{f}={500}\) and \(t_{\ell }={2000}\). The contig with maximum length (Max) is reported in the number of fragments and the total genomic length in mega base pairs (Mbp). Similarly, the mean contig length (Mean) is also reported in the number of fragments and the total genomic length in mega base pairs. The genome fraction (GF) is the percentage of the genome that is covered by at least one contig. Lastly, the number of mis-assembled contigs (MA) is given