Table 6.
Simulated low coverage datasets analysis where the inputs of EIM pipeline are the read set and genome reconstructed by Bowtie2
| Assembly | Exact | EIM (v2) | Bowtie2 | Exact | EIM (v2) | Bowtie2 | |
|---|---|---|---|---|---|---|---|
| DWGSIM simulator | ART simulator | ||||||
| ReadSet5 | ReadSet9 | ||||||
| Contigs-500 | 172 | 14 | 58 | 137 | 13 | 56 | |
| N50 (kbp) | 43.9 | 735.7 | 159.6 | 75.2 | 909.5 | 175.3 | |
| Errors | 0 | 53 | 64 | 1 | 45 | 53 | |
| IUPAC-codes | 0 | 36 | 137 | 0 | 38 | 102 | |
| Genome-Fraction (%) | 98.899 | 99.991 | 99.983 | 98.912 | 99.983 | 99.965 | |
| ReadSet6 | ReadSet10 | ||||||
| Contigs-500 | 163 | 6 | 64 | 178 | 18 | 63 | |
| N50 (kbp) | 44.4 | 1698.5 | 112.2 | 45.4 | 485.2 | 116.9 | |
| Errors | 1 | 68 | 92 | 2 | 68 | 83 | |
| IUPAC-codes | 0 | 28 | 95 | 0 | 39 | 187 | |
| Genome-Fraction (%) | 98.843 | 99.998 | 99.976 | 98.871 | 99.988 | 99.984 | |
| ReadSet7 | ReadSet11 | ||||||
| Contigs-500 | 424 | 11 | 55 | 425 | 17 | 70 | |
| N50 (kbp) | 16.6 | 590.9 | 125.9 | 18 | 386.6 | 115.4 | |
| Errors | 2 | 185 | 361 | 6 | 179 | 369 | |
| IUPAC-codes | 0 | 24 | 117 | 0 | 38 | 151 | |
| Genome-Fraction (%) | 98.666 | 99.993 | 99.985 | 98.697 | 99.989 | 99.983 | |
| ReadSet8 | ReadSet12 | ||||||
| Contigs-500 | 397 | 17 | 56 | 366 | 13 | 49 | |
| N50 (kbp) | 18.9 | 493.4 | 141.1 | 21.6 | 529.5 | 127.6 | |
| Errors | 8 | 190 | 331 | 8 | 186 | 322 | |
| IUPAC-codes | 0 | 21 | 105 | 0 | 23 | 121 | |
| Genome-Fraction (%) | 98.771 | 99.99 | 99.979 | 98.799 | 99.983 | 99.982 |
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. The results of running the pipeline on datasets simulated by DWGSIM and ART are shown in left and right side of the table, respectively