Table 2 Comparison of running times among methods
From: Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data
Run accession | ERR188074 | ERR188125 | ERR188171 | ERR188362 | |
|---|---|---|---|---|---|
Run and mapping statics | Number of reads | 31,540,813 | 28,810,860 | 30,386,179 | 26,255,381 |
Length of reads | 75 | 75 | 75 | 75 | |
Bowtie mapping rate | 84.7% | 80.2% | 84.6% | 80.4% | |
CPU time comparison (s)a | eXpress | 14,546.6 | 24,036.1 | 13,429.5 | 23,103.9 |
RSEM | 22,700.6 | 20,545.9 | 21,753.1 | 18,842.2 | |
Bowtie | 1487.8 | 1477.5 | 1472.6 | 1319.5 | |
Sailfish | 299.0 | 281.0 | 294.2 | 285.5 | |
Kallisto | 138.7 | 144.2 | 136.7 | 129.5 | |
Matataki | 57.2 | 46.4 | 43.9 | 42.5 | |
Acceleration rate compared with existing methods | eXpress | 254 | 517 | 305 | 543 |
RSEM | 397 | 442 | 495 | 443 | |
Bowtie | 26.0 | 31.8 | 33.5 | 31.0 | |
Sailfish | 5.23 | 6.05 | 6.69 | 6.71 | |
Kallisto | 2.43 | 3.107 | 3.11 | 3.05 | |