Table 5.
Simulated high coverage datasets analysis where the inputs of EIM pipeline are the read set and genome reconstructed by Bowtie2
| Assembly | Exact | EIM (v2) | Bowtie2 |
|---|---|---|---|
| ReadSet1 | |||
| Contigs-500 | 68 | 2 | 6 |
| N50 (kbp) | 156.4 | 3543.3 | 2385.6 |
| Errors | 0 | 29 | 38 |
| IUPAC-codes | 0 | 11 | 137 |
| Genome-Fraction (%) | 99.381 | 99.999 | 100 |
| ReadSet2 | |||
| Contigs-500 | 142 | 3 | 5 |
| N50 (kbp) | 62.7 | 1371.6 | 939.1 |
| Errors | 0 | 45 | 92 |
| IUPAC-codes | 0 | 29 | 246 |
| Genome-Fraction (%) | 99.338 | 100 | 99.997 |
| ReadSet3 | |||
| Contigs-500 | 96 | 6 | 3 |
| N50 (kbp) | 94.4 | 1096.2 | 3267.7 |
| Errors | 2 | 54 | 87 |
| IUPAC-codes | 0 | 11 | 140 |
| Genome-Fraction (%) | 99.285 | 99.997 | 100 |
| ReadSet4 | |||
| Contigs-500 | 77 | 3 | 3 |
| N50 (kbp) | 115.5 | 2337.4 | 1530.2 |
| Errors | 6 | 55 | 72 |
| IUPAC-codes | 0 | 15 | 34 |
| Genome-Fraction (%) | 99.436 | 99.998 | 100 |
The evaluation metrics has been defined in the text. The columns headed ’Exact’, ’EIM (v2)’ and ’Bowtie2’ represent the contiguity and quality of contigs constructed by ExactMapping step of EIM, EIM (v2) and Bowtie2, respectively