Table 2 Evaluation of error correction performance
From: HALC: High throughput algorithm for long read error correction
Method | Throughput | Alignment ratio | Alignment identity | Genome fraction | N reads | Average read length | Sensitivity | Gain | Specificity |
|---|---|---|---|---|---|---|---|---|---|
(a) Long reads of E. coli | |||||||||
Initial | 100.0% | 50.4% | 95.2% | 100.0% | 75152 | 2381 | - | - | - |
PacBioToCAa | 24.2% | 100.0% | 100.0% | 99.5% | 53447 | 810 | - | - | - |
LSC | 53.5% | 98.7% | 99.9% | 99.7% | 115960 | 825 | 52.6% | 51.7% | 99.9% |
Proovread | 57.4% | 100.0% | 99.9% | 99.7% | 44986 | 2284 | 57.4% | 56.8% | 99.9% |
CoLoRMap | 42.8% | 99.7% | 100.0% | 99.9% | 70582 | 1084 | 42.7% | 42.2% | 99.9% |
ECTools | 23.5% | 99.9% | 99.2% | 99.4% | 8095 | 5211 | 23.4% | 21.8% | 99.8% |
LoRDEC | 60.8% | 97.8% | 100.0% | 99.8% | 70164 | 1549 | 60.7% | 60.5% | 100.0% |
Jabba | 52.8% | 99.6% | 100.0% | 98.6% | 26459 | 3568 | 52.8% | 52.7% | 100.0% |
HALC | 64.6% | 98.6% | 99.9% | 99.8% | 78731 | 1467 | 64.4% | 64.0% | 99.9% |
(b) Long reads of A. thaliana | |||||||||
Initial | 100.0% | 32.4% | 92.4% | 82.4% | 490418 | 2645 | - | - | - |
PacBioToCAa | 10.7% | 99.2% | 99.7% | 63.9% | 260834 | 535 | - | - | - |
LSC | 25.9% | 100.0% | 99.5% | 71.4% | 659123 | 509 | 24.2% | 22.3% | 99.7% |
Proovread | 27.8% | 99.8% | 99.7% | 79.8% | 125786 | 2864 | 26.5% | 24.9% | 99.7% |
CoLoRMap | 21.4% | 99.4% | 99.7% | 69.3% | 230933 | 1203 | 20.5% | 19.2% | 99.8% |
ECTools | 11.3% | 99.8% | 99.5% | 63.1% | 21354 | 6886 | 10.8% | 9.8% | 99.8% |
LoRDEC | 28.0% | 86.4% | 99.5% | 74.4% | 847963 | 428 | 25.9% | 22.8% | 99.6% |
Jabba | 10.8% | 99.6% | 99.7% | 56.1% | 51353 | 2726 | 10.5% | 9.9% | 99.9% |
HALC | 34.7% | 96.5% | 99.5% | 85.8% | 548872 | 819 | 33.2% | 29.7% | 99.3% |
(c) Long reads of Maylandia zebra | |||||||||
Initial | 100.0% | 46.9% | 91.3% | 91.9% | 1307812 | 10082 | - | - | - |
LoRDEC | 33.6% | 97.9% | 99.7% | 89.5% | 7372455 | 601 | 32.4% | 29.8% | 99.6% |
HALC | 41.2% | 98.7% | 99.6% | 90.7% | 4833536 | 1123 | 40.2% | 37.5% | 99.4% |