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Table 3 Running time and memory usage of quantification methods on SE and PE data

From: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

  SE PE
Method Alignment time Quant. time Total time Peak Memory Alignment time Quant. time Total time Peak Memory
RSEM 24 50 74 1.1 15 50 66 1.1
IsoEM 5 6 12 12 14 10 24 14
Cufflinks 33 3 36 2.0 60 6 66 2.0
rQuant 33 183 216 2.0     
RSEM v0.6 9 22 31 1.1     
  1. The alignment time, quantification time, total time, and peak memory usage of the tested quantification methods on SE and PE simulated data sets with 20 million fragments. Times are in minutes and memory is specified in GB.