Table 2 Error correction benchmarking results for simulated Oxford Nanopore reads of various polyploid genomes (ploidy = 2, 3, 4)
From: VeChat: correcting errors in long reads using variation graphs
Method | #Reads | Error rate (%) | Mismatch (%) | Indel (%) | Haplotype coverage (%) | N50 (bp) | NGA50 (bp) | #Misassemblies |
|---|---|---|---|---|---|---|---|---|
Ploidy = 2 | ||||||||
VeChat | 30920 | 0.022 | 0.007 | 0.014 | 99.9 | 13,095 | 40,612 | 5 |
CONSENT | 32661 | 0.212 | 0.160 | 0.052 | 99.9 | 13,040 | 40,903 | 37 |
Racon | 31840 | 0.346 | 0.234 | 0.112 | 99.3 | 13,039 | 40,725 | 120 |
Canu | 25506 | 0.390 | 0.206 | 0.183 | 100.0 | 13,820 | 40,846 | 6 |
Daccord | 31438 | 0.438 | 0.410 | 0.027 | 99.2 | 12,987 | 40,730 | 3 |
Ploidy = 3 | ||||||||
VeChat | 45113 | 0.090 | 0.041 | 0.050 | 100.0 | 13,130 | 40,497 | 90 |
CONSENT | 49826 | 0.298 | 0.221 | 0.077 | 99.9 | 13,037 | 40,877 | 103 |
Racon | 48520 | 0.673 | 0.501 | 0.172 | 98.6 | 13,028 | 39,286 | 631 |
Canu | 36962 | 0.748 | 0.453 | 0.295 | 99.9 | 14,141 | 40,605 | 59 |
Daccord | 49033 | 0.821 | 0.751 | 0.069 | 99.7 | 12,712 | 39,193 | 11 |
Ploidy = 4 | ||||||||
VeChat | 58739 | 0.169 | 0.098 | 0.071 | 99.7 | 13,129 | 40,450 | 177 |
CONSENT | 65384 | 0.292 | 0.195 | 0.097 | 100.0 | 13,033 | 40,864 | 121 |
Racon | 63670 | 0.666 | 0.469 | 0.197 | 94.9 | 13,012 | 40,007 | 668 |
Daccord | 65072 | 0.840 | 0.784 | 0.056 | 96.9 | 12,606 | 39,076 | 22 |
