Table 2 Benchmarking results for PacBio CLR data
From: phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
Dataset | Assembler | Size (Mb) | HC (%) | k-mer recovery(%) | Continuity (bp) | QV | Switch error(%) | N (%) | Dup (%) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | All | Mat | Pat | NG50 | NGA50 | Phased N50 | Â | Â | Â | Â |
MHC (CLR 25x) | phasebook | 10.8 | 95.2 | 96.7 | 88.0 | 76.3 | 172,577 | 172,577 | 133,141 | 37.7 | 0.66 | 0.0 | 1.36 |
| Â | phasebook-hi | 14.3 | 98.0 | 97.5 | 89.4 | 88.8 | 361,721 | 354,437 | 122,594 | 40.6 | 6.26 | 0.0 | 1.88 |
| Â | Canu | 5.9 | 59.2 | 96.3 | 80.7 | 76.9 | 2,184,005 | 62,395 | 65,217 | 39.4 | 4.57 | 0.0 | 0.92 |
| Â | Falcon | 5.4 | 60.5 | 94.3 | 82.2 | 68.8 | 4,814,264 | 32,719 | 120,818 | 27.6 | 5.24 | 0.0 | 1.17 |
| Â | Flye | 5.0 | 74.1 | 94.2 | 64.2 | 70.5 | 548,628 | 66,242 | 74,992 | 37.1 | 5.34 | 0.0 | 1.01 |
|  | Wtdbg2 | 4.7 | 58.9 | 90.5 | 46.9 | 63.2 | – | – | 102,431 | 33.0 | 5.49 | 0.0 | 0.93 |
| Â | HapCut2 | 9.1 | 56.4 | 84.2 | 53.7 | 53.0 | 393,164 | 254,386 | 282,817 | 31.3 | 5.93 | 8.9 | 1.52 |
| Â | WhatsHap | 9.2 | 56.6 | 84.2 | 53.4 | 53.2 | 393,164 | 254,386 | 279,136 | 31.2 | 5.62 | 8.8 | 1.52 |
HG00733 (Chr6) (CLR 44x) | phasebook | 453.2 | 92.9 | 98.7 | 89.7 | 90.6 | 256,934 | 253,785 | 164,373 | 32.6 | 5.50 | 0.0 | 1.92 |
| Â | phasebook-hi | 291.0 | 81.0 | 97.9 | 68.2 | 65.3 | 587,151 | 552,300 | 201,382 | 33.9 | 14.41 | 0.0 | 1.33 |
|  | Canu | 178.0 | 56.8 | 97.9 | 52.7 | 52.9 | 110,328 | – | 119,821 | 38.8 | 17.57 | 0.0 | 0.98 |
| Â | Falcon | 185.6 | 63.4 | 95.1 | 41.8 | 42.0 | 155,444 | 132,950 | 142,167 | 28.6 | 22.22 | 0.0 | 1.04 |
|  | Flye | 168.1 | 51.9 | 97.6 | 25.4 | 75.8 | – | – | 2,094,032 | 42.9 | 3.12 | 0.0 | 0.99 |
|  | Wtdbg2 | 165.2 | 64.6 | 88.9 | 35.3 | 35.3 | – | – | 142,300 | 24.2 | 20.07 | 0.0 | 1.0 |
| Â | HapCut2 | 341.3 | 61.8 | 99.3 | 92.1 | 91.7 | 3,899,799 | 1,944,878 | 1,346,888 | 41.0 | 5.65 | 0.4 | 1.57 |
| Â | WhatsHap | 341.3 | 63.4 | 99.3 | 92.1 | 91.6 | 3,349,274 | 1,944,877 | 1,334,202 | 40.9 | 5.72 | 0.4 | 1.53 |
HG002 (CLR 25x) | phasebook | 5829 | – | 92.3 | 60.1 | 59.2 | 96,740 | – | 70,473 | 31.9 | 1.61 | 0.0 | – |
|  | phasebook-hi | 6590 | – | 97.1 | 62.0 | 70.6 | 312,775 | – | 150,123 | 35.2 | 7.16 | 0.0 | – |
|  | Canu | 3119 | – | 97.1 | 49.5 | 62.3 | 47,412 | – | 207,853 | 40.0 | 6.49 | 0.0 | – |
|  | HapCut2 | 6435 | – | 98.8 | 87.9 | 90.2 | 145,138,636 | – | 1,756,246 | 40.1 | 1.52 | 5.4 | – |
|  | WhatsHap | 6435 | – | 98.8 | 87.9 | 90.2 | 145,138,636 | – | 1,729,580 | 40.1 | 1.52 | 5.4 | – |
A. thaliana (CLR 75x) | phasebook | 301 | – | 89.7 | 76.6 | 76.0 | 66,120 | – | 39,513 | 27.0 | 2.78 | 0.0 | – |
|  | phasebook-hi | 296 | – | 94.9 | 89.5 | 88.8 | 301,078 | – | 149,964 | 33.4 | 4.25 | 0.0 | – |
|  | Canu | 238 | – | 94.4 | 86.8 | 86.6 | 204,191 | – | 64,998 | 31.9 | 4.88 | 0.0 | – |
|  | Flye | 142 | – | 87.1 | 62.8 | 62.5 | 35,796 | – | 30,209 | 30.0 | 7.54 | 0.0 | – |
|  | Wtdbg2 | 125 | – | 35.1 | 26.4 | 26.3 | 11,374 | – | 35,733 | 14.4 | 15.17 | 0.0 | – |
|  | HapCut2 | 238 | – | 91.3 | 99.4 | 53.3 | 18,585,056 | – | 531,267 | 36.4 | 5.73 | 0.2 | – |
|  | WhatsHap | 238 | – | 91.3 | 99.5 | 53.3 | 1,8585,056 | – | 1,637,965 | 36.3 | 5.72 | 0.2 | – |