Table 2 Comparison of assembly-based metrics (with % improvement) evaluated from testing E. coli: with downsampled short reads (D-SR) having 18x coverage (lowest coverage) and original short reads, E. coli (Sequel-sequenced) S. cerevisiae, A. funestus (merged flowcells) on proovread, LoRDEC, CoLoRMap, and HECIL.
From: HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
Data | Evaluation Metric | Original | proovread | LoRDEC | CoLoRMap | HECIL (Iter 1) | HECIL (Iter 5) |
|---|---|---|---|---|---|---|---|
E. coli (D-SR) | # Contigs | 182 | 29 (84.0) | 28 (84.6) | 24 (86.8) | 20 (89.0) | — |
Largest contig | 69,266 | 567,484 (719.2) | 885,819 (1178.8) | 813,262 (1074.1) | 1,204,631 (1639.1) | — | |
Total length | 3,508,197 | 4,235,031 (20.7) | 4,068,085 (15.9) | 4,036,161 (15.0) | 4,596,013 (31.0) | — | |
N50 | 24,663 | 189,712 (669.2) | 179,638 (628.3) | 184,367 (647.5)) | 232,826 (844.0) | — | |
NG50 | 17,847 | 212,621 (1091.3) | 190,621 (968.0) | 210,913 (1081.7) | 267,311 (1397.7) | — | |
Aligned base (%) - Ref/Query | 83/84 | 87/89 | 92/93 | 48/92 | 97/100 | — | |
Average Identity (1–1) - Ref/Query | 88/88 | 93/93 | 97/97 | 97/97 | 99/99 | — | |
E. coli | # Contigs | 182 | 26 (85.7) | 24 (86.8) | 19 (89.5) | 19 (89.5) | 17 (90.6) |
Largest contig | 69,266 | 605,792 (774.5) | 920,903 (1229.5) | 1,089,140 (1472.4) | 1,223,474 (1666.3) | 1,481,824 (2039.3) | |
Total length | 3,508,197 | 4,629,719 (31.9) | 4,623,137 (31.7) | 4,624,793 (31.8) | 4,838,971 (37.9) | 5,106,276 (45.5) | |
N50 | 24,663 | 231,774 (839.7) | 226,456 (818.2) | 239,066 (869.3) | 256,830 (941.3) | 288,192 (1068.5) | |
NG50 | 17,847 | 231,774 (1198.6) | 226,456 (1168.8) | 239,066 (1239.5) | 294,635 (1550.8) | 344,848 (1832.2) | |
Aligned base (%) - Ref/Query | 82/87 | 92/92 | 98/98 | 54/94 | 99/99 | 99/99 | |
Average Identity (1–1) - Ref/Query | 91/91 | 95/95 | 96/96 | 97/97 | 98/98 | 99/99 | |
E. coli (Sequel) | # Contigs | 84 | 34 (59.5) | 29 (65.4) | 29 (65.4) | 27 (67.8) | 24 (71.4) |
Largest contig | 88,975 | 775,707 (771.8) | 884,469 (894.0) | 1,363,678 (1432.6) | 1,627,011 (1728.6) | 1,865,932 (1997.1) | |
Total length | 5,389,574 | 6,012,453 (11.5) | 5,821,596 (8.0) | 5,819,632 (7.9) | 6,374,798 (18.2) | 6,773,369 (25.6) | |
N50 | 18,611 | 119,735 (543.3) | 117,028 (528.8) | 127,892 (587.1) | 141,213 (658.7) | 162,580 (773.5) | |
NG50 | 13,903 | 116,255 (736.1) | 113,036 (713.0) | 118,087 (749.3) | 122,389 (780.3) | 149,637 (976.2) | |
Aligned base (%) - Ref/Query | 78/80 | 89/89 | 95/95 | 67/92 | 97/97 | 98/98 | |
Average Identity (1–1) - Ref/Query | 88/88 | 92/92 | 92/92 | 93/93 | 95/96 | 98/98 | |
S. cerevisiae | # Contigs | 26 | 32 (−23.0) | 28 (−7.6) | 24 (7.6) | 24 (7.6) | 23 (11.5) |
Largest contig | 1,543,990 | 1,537,979 (−0.3) | 1,552,711 (0.5) | 1,555,857 (0.7) | 1,558,190 (0.9) | 1,713,201 (10.9) | |
Total length | 12,341,981 (1.1) | 12,485,995 (1.1) | 12,497,078 (1.2) | 12,315,869 (−0.2) | 12,435,702 (0.7) | 12,731,203 (3.1) | |
N50 | 777,602 | 777,713 (0.0) | 818,962 (5.3) | 932,935 (19.9) | 1,018,591 (30.9) | 1,308,313 (68.2) | |
NG50 | 777,602 | 777,713 (0.0) | 818,962 (5.3) | 932,935 (19.9) | 1,538,190 (97.8) | 2,005,346 (157.8) | |
Aligned base (%) - Ref/Query | 95/90 | 91/91 | 95/95 | 78/97 | 99/99 | 99/99 | |
Average Identity (1–1) - Ref/Query | 92/92 | 93/93 | 97/97 | 98/98 | 99/99 | 99/99 | |
A. funestus | # Contigs | 998 | 712 (28.6) | 788 (21.0) | 847 (15.1) | 633 (36.5) | 543 (45.5) |
Largest contig | 71,070 | 36,306 (−48.9) | 75,298 (5.9) | 72,306 (1.7) | 84,490 (18.8) | 94,937 (33.5) | |
Total length | 25,405,949 | 8,371,287 (−67.0) | 26,745,092 (5.2) | 26,802,126 (5.5) | 28,954,268 (13.9) | 32,371,298 (27.4) | |
N50 | 13,038 | 14,802 (13.5) | 15,118 (15.9) | 14,555 (11.6) | 16,409 (25.8) | 19,014 (45.8) | |
NG50 | 71,070 | 45,637 (−35.7) | 77,294 (8.7) | 76,306 (7.3) | 84,490 (18.8) | 91,303 (28.4) | |
Aligned base (%) - Ref/Query | 20/87 | 23/93 | 27/96 | 20/95 | 31/99 | 37/99 | |
Average Identity (1–1) - Ref/Query | 83/83 | 87/87 | 95/95 | 92/92 | 98/98 | 99/99 |
