Table 2.
Run-time and Memory Usage Comparison of Mashmap Against Minimap, Burrows–Wheeler Aligner-MEM and Basic Local Alignment with Successive Refinement for N1, P1 Datasets
| N1 (MinION-K12) | P1 (Pacbio-CHM1) | |||||
|---|---|---|---|---|---|---|
| Method | Index | Map | Memory (MB) | Index | Map | Memory (GB) |
| Mashmap | 0.5 seconds | 54 seconds | 17 | 5 minutes 52 seconds | 1 minutes 24 seconds | 3.7 |
| Minimap | 0.7 seconds | 37 seconds | 232 | 3 minutes 7 seconds | 1 minute 56 seconds | 6.8 |
| BWA-MEM | 2.6 seconds | 5 hours 39 minutes | 72 | 1 hours 19 minutes | 6 hours 46 minutes | 5.5 |
| BLASR | 1.3 seconds | 10 hours 17 minutes | 697 | 40 minutes 36 seconds | 20 hours 40 minutes | 17.6 |
BWA-MEM was executed with long-read mapping parameters-x pacbio/ont2d.
BWA, Burrows–Wheeler Aligner.
The best results are highlighted in bold.