Table 1: Sensitivity, precision, run times and memory usage of leading spliced aligners.
|
Program |
Sensitivity (%) |
Precision (%) |
Run time (min) |
Memory usage (GB) |
|
HISAT2 |
97.3 |
94.8 |
26.7 |
4.3 |
|
TopHat2 |
90.6 |
82.6 |
1,170 |
4.3 |
|
STAR |
96.3 |
88.3 |
25 |
28 |
|
Bowtie2 |
91.1 |
79.2 |
13 |
14 |
Sensitivity, precision, run times and memory usage of leading spliced aligners for 87,944 true splice sites contained in 30 million simulated reads from the human genome, with a mismatch rate of 0.5%. We used three CPU cores to run the programs on a Mac Pro with a 3.7 GHz Quad-Core Intel Xeon E5 processor and 64 GB of RAM.