SCA
Self-correction approach (SCA) was proposed in the ref (Reducing assembly complexity of microbial genomes with single-molecule sequencin, Genome Biology 2013).
DataSet1
We used all SMRT cells and randomly selected four and six SMRT cells three times for each, and access the correctness by Quast.
Performance
| Statistics without reference | All Data | 4 SMRT cells : 1st Set | 4 SMRT cells : 2nd Set | 4 SMRT cells : 3rd Set | 6 SMRT cells : 1st Set | 6 SMRT cells : 2nd Set | 6 SMRT cells : 3rd Set |
| # contigs | 16 | 10 | 14 | 16 | 9 | 18 | 13 |
| Largest contig | 2 198 457 | 3 4848 77 | 1 936 831 | 1 948 632 | 2 104 087 | 1 169 224 | 1 439 551 |
| Total length | 4 808 733 | 4 706 800 | 4 705 398 | 4 745 036 | 4 741 512 | 4 814 718 | 4 749 785 |
| N50 | 1 005 770 | 3 484 877 | 966 809 | 1 434 284 | 1 655 500 | 676 526 | 1 268 010 |
| Misassemblies | |||||||
| # misassemblies | 19 | 9 | 12 | 15 | 14 | 17 | 11 |
| Misassembled contigs length | 2 939 040 | 3 530 352 | 2 949 761 | 3 653 461 | 3 820 624 | 2 387 129 | 3 986 402 |
| Mismatches | |||||||
| # mismatches per 100kbp | 0.8 | 0.43 | 0.58 | 1.36 | 0.15 | 0.95 | 0.58 |
| # indels per 100kbp | 5.71 | 2.98 | 4.45 | 9.56 | 1.77 | 8.02 | 6.88 |
| # N's per 100kbp | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Genome Statistics | |||||||
| Genome fraction(%) | 100 | 100 | 99.815 | 99.87 | 100 | 99.995 | 99.979 |
| Duplication ratio | 1.037 | 1.016 | 1.017 | 1.025 | 1.022 | 1.038 | 1.025 |
| # genes | 4494+3 part | 4494+3 part | 4480+7 part | 4485+9 part | 4494+3 part | 4493+4 part | 4492+5 part |
| NGA50 | 615 234 | 1 205 052 | 572 342 | 875 953 | 844 482 | 633 220 | 1 267 242 |
| Running Time | 19hr 06m | 13hr 34m | 13hr 21m | 12hr 38m | 21hr 28m | 22hr 56m | 22hr 07m |