Table 1 Experimental results for E. coli PacBio data set D1-P
From: A comprehensive evaluation of long read error correction methods
Method | # Reads | # Bases | # Aligned | # Aligned | Maximum | N50 | Genome | Alignment | CPU time | Wall time | Memory |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | (Mbp) | reads | bases (Mbp) | length (bp) | (bp) | fraction (%) | identity(%) | (hh:mm:ss) | (hh:mm:ss) | usage (GB) |
Original | 85460 | 748.0 | 82886 | 688.0 | 44113 | 13990 | 100.000 | 86.8763 | - | - | - |
Non-hybrid methods | |||||||||||
FLAS | 69327 | 632.3 | 68786 | 621.2 | 40117 | 13212 | 100.000 | 99.5959 | 09:47:50 | 00:56:45 | 4.9 |
LoRMA | 330811 | 623.3 | 330715 | 623.0 | 22499 | 2441 | 100.000 | 99.6814 | 45:24:49 | 02:10:36 | 67.2 |
Canu | 9283 | 168.1 | 9193 | 166.7 | 39693 | 20391 | 100.000 | 99.6970 | 07:47:33 | 00:27:14 | 6.0 |
Short-read-assembly-based methods | |||||||||||
HG-CoLoR | - | - | - | - | - | - | - | - | - | - | - |
FMLRC | 85260 | 706.5 | 83320 | 669.9 | 44084 | 13364 | 100.000 | 99.6983 | 03:05:06 | 00:30:07 | 9.8 |
HALC | 85256 | 711.1 | 84030 | 661.7 | 44117 | 13399 | 100.000 | 99.4374 | 60:41:59 | 16:02:32 | 30.2 |
Jabba | 77508 | 620.2 | 77508 | 619.7 | 41342 | 12557 | 99.258 | 99.9624 | 02:05:09 | 00:12:01 | 37.0 |
LoRDEC | 85324 | 716.9 | 83507 | 665.9 | 44311 | 13491 | 100.000 | 98.4149 | 15:03:42 | 00:40:05 | 2.0 |
ECTools | 55687 | 577.4 | 55687 | 575.7 | 39772 | 13583 | 100.000 | 99.8592 | 11:25:22 | 00:29:49 | 8.2 |
Short-read-alignment-based methods | |||||||||||
Hercules | - | - | - | - | - | - | - | - | - | >72:00:00 | - |
CoLoRMap | 85674 | 730.7 | 83765 | 678.6 | 44113 | 13641 | 100.000 | 95.2930 | 31:35:16 | 02:53:33 | 34.9 |
Nanocorr | 73368 | 504.9 | 73316 | 493.1 | 41079 | 10796 | 100.000 | 98.3257 | 1862:59:19 | 70:57:19 | 15.1 |
proovread | 85367 | 720.2 | 83142 | 665.7 | 44113 | 13524 | 100.000 | 96.7250 | 71:17:14 | 12:21:53 | 53.9 |
LSC | - | - | - | - | - | - | - | - | - | >72:00:00 | - |