Table 1

Simulated 36 bp E. coli

Corrections

Trim corrections

Mis-corrections

Error reads kept

Time (min)


Quake

1035709.4

26337.0

1744.0

5537.0

14.2

SOAPdenovo

969666.4

120529.0

3912.8

9288.4

12.4

Shrec

964431.8

0.0

165422.0

41733.6

87.6


Simulated E. coli 36 bp reads at 40× coverage averaged over five runs. For each method, we counted the number of reads that were properly corrected to their original state (Corrections), trimmed such that no errors remained (Trim corrections), mis-corrected to false sequence (Mis-corrections), and contained errors but were kept in the set (Error reads kept). Quake corrects more reads while mis-correcting fewer reads and keeping fewer reads with errors than all programs.

Kelley et al. Genome Biology 2010 11:R116   doi:10.1186/gb-2010-11-11-r116

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