Table 4 Results of the error correction experiment
From: GraphAligner: rapid and versatile sequence-to-graph alignment
Dataset | Method | # Reads | Bases (Mbp) | Aligned reads (%) | Aligned bases (%) | N50 (bp) | Genome fraction (%) | Error rate (%) | CPU time (hh:mm:ss) | Peak memory (GB) |
|---|---|---|---|---|---|---|---|---|---|---|
E. coli | Original | 85460 | 748.0 | 97.0 | 92.0 | 13990 | 100 | 13.1237 | - | - |
PacBio | LoRDEC | 85316 | 716.5 | 97.9 | 92.9 | 13484 | 100 | 1.3902 | 10:11:28 | 5.0 |
LoRDEC-clip | 129754 | 654.5 | 99.9 | 99.8 | 8206 | 100 | 0.0881 | 10:11:28 | 5.0 | |
FMRLC | 85260 | 706.5 | 97.7 | 94.8 | 13364 | 100 | 0.3016 | 4:16:43 | 2.6 | |
GraphAligner | 85271 | 710.7 | 97.7 | 93.9 | 13411 | 100 | 0.5057 | 0:23:08 | 5.8 | |
GraphAligner- clip | 91909 | 673.9 | 99.9 | 99.8 | 12146 | 100 | 0.0240 | 0:23:08 | 5.8 | |
Fruit fly | Original | 642255 | 4609.5 | 84.4 | 82.5 | 11956 | 98.77 | 16.1650 | - | - |
ONT | FMRLC | 641956 | 4646.9 | 89.6 | 85.1 | 12087 | 98.62 | 2.3250 | 65:17:52 | 9.2 |
GraphAligner | 640548 | 4653.7 | 90.7 | 85.6 | 12109 | 98.63 | 1.2433 | 15:12:30 | 11.9 | |
GraphAligner- clip | 762073 | 4188.3 | 99.3 | 94.7 | 8698 | 97.86 | 0.7087 | 15:12:30 | 11.9 | |
HG00733 | Original | 2394990 | 48801.0 | 95.6 | 92.8 | 33109 | 95.27 | 13.5384 | - | - |
PacBio | FMRLC | 2392533 | 48229.9 | 98.3 | 92.7 | 32823 | 95.19 | 7.1210 | 2222:13:44 | 234.5 |
GraphAligner | 2390656 | 48216.2 | 98.1 | 94.6 | 32879 | 94.89 | 3.3510 | 174:54:13 | 76.7 | |
GraphAligner-clip | 8252956 | 42292.0 | 99.8 | 98.3 | 7973 | 91.91 | 1.3503 | 174:54:13 | 76.7 |