Table 1.
Error correction with multiple short read coverages
| CH17-157L1 BAC clone – number of aligned reads | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10× | 20× | 30× | ||||||||||
| Tool | Mapped | 80–90% | 90–95% | >95% | Mapped | 80–90% | 90–95% | >95% | Mapped | 80–90% | 90–95% | >95% |
| Uncorrected | 33 842 | 17 582 | 1 974 | 461 | 33 842 | 17 582 | 1 974 | 461 | 33 842 | 17 582 | 1 974 | 461 |
| Colormap | 34 215 | 15 622 | 4 979 | 1 579 | 34 515 | 14 882 | 5 989 | 2 585 | 34 710 | 14 428 | 6 528 | 3 263 |
| HALC (w/ LoRDEC) | 33 933 | 17 656 | 1 870 | 569 | 35 287 | 13 250 | 5 708 | 5 390 | 37 217 | 12 040 | 6 948 | 8 845 |
| HALC (w/o LoRDEC) | 33 908 | 17 662 | 1 867 | 537 | 34 242 | 17 919 | 1 627 | 816 | 34 908 | 18 360 | 1 986 | 1 360 |
| Hercules | 36 585 | 14 539 | 6 675 | 3 917 | 40 863 | 14 165 | 7 067 | 8 498 | 41 549 | 13 880 | 7 162 | 9 631 |
| LoRDEC | 36 604 | 13 752 | 7 050 | 6 270 | 37 098 | 11 249 | 7 302 | 10 953 | 36 965 | 10 597 | 7 157 | 12 118 |
| LSC | 35 991 | 14 465 | 6 234 | 3 939 | 40 368 | 13 939 | 6 901 | 8 571 | 41 254 | 13 774 | 6 957 | 9 788 |
| proovread | 34 191 | 16 881 | 3 301 | 1 013 | 34 361 | 16 534 | 3 851 | 1 380 | 34 604 | 16 324 | 4 223 | 1 821 |
| CH17-227A2 BAC clone - Number of aligned reads | ||||||||||||
| Uncorrected | 45 625 | 25 356 | 7 385 | 219 | 45 625 | 25 356 | 7 385 | 219 | 45 625 | 25 356 | 7 385 | 219 |
| Colormap | 45 679 | 22 878 | 9 295 | 1 223 | 45 712 | 21 701 | 9 897 | 2 072 | 45 758 | 21 019 | 10 269 | 2 590 |
| HALC (w/ LoRDEC) | 45 772 | 25 460 | 7 058 | 627 | 46 929 | 14 570 | 8 843 | 14 061 | 48 682 | 13 118 | 9 207 | 18 122 |
| HALC (w/o LoRDEC) | 45 679 | 22 878 | 9 295 | 1 223 | 45 943 | 26 399 | 6 414 | 656 | 47 038 | 25 223 | 8 453 | 1 833 |
| Hercules | 50 090 | 15 883 | 11 007 | 13 256 | 54 551 | 14 800 | 10 546 | 19 741 | 54 666 | 14 421 | 10 329 | 20 645 |
| LoRDEC | 46 467 | 14 787 | 10 010 | 13 053 | 46 893 | 11 422 | 8 301 | 20 332 | 46 956 | 10 329 | 7 719 | 22 597 |
| LSC | 50 162 | 16 206 | 11 727 | 12 385 | 53 762 | 15 071 | 10 805 | 18 568 | 53 887 | 14 624 | 10 578 | 19 501 |
| proovread | 45 700 | 23 444 | 8 869 | 1 139 | 45 797 | 22 612 | 9 289 | 1 833 | 45 919 | 22 044 | 9 467 | 2 489 |
We applied Hercules to correct PacBio reads generated from two BAC clones (CH17-157L1 and CH17-227A2) using Illumina reads from the same resource. We subsampled the Illumina reads into 10×, 20× and 30× to test the performance of the tools for both low and moderate short read coverage. We report the accuracy as the alignment identity as calculated by the BLASR (34) aligner. Mapped refers to the number of any reads aligned to the Sanger-assembled reference for these clones with any identity, where the other columns show the number of alignments within respective identity brackets.