Table 4.
Simulated ReadSet1 analysis where the inputs of EIM pipeline are the read set and either the reference genome (ref) or the genome reconstructed by Bowtie2 (cns-bt)
| c 1 | c 2 | c 3 | c 4 | c 5 | c 6 | c 7 |
|---|---|---|---|---|---|---|
| Assembly | Exact | EIM | Exact | EIM (v1) | EIM (v2) | Bowtie2 |
| /ref | /ref | /cns-bt | /cns-bt | /cns-bt | / ref | |
| Contigs-500 | 2817 | 1 | 68 | 9 | 2 | 6 |
| N50 (kbp) | 1.82 | 4639.6 | 156.4 | 1108.9 | 3543.3 | 2385.650 |
| Errors | 3 | 45 | 0 | 28 | 29 | 38 |
| Genome-Fraction (%) | 90.285 | 100 | 99.381 | 99.992 | 99.999 | 100 |
The evaluation metrics has been defined in the text. The columns headed ’Exact/ref’, ’EIM/ref’, ’EIM (v1)/cns-bt’, ’EIM (v2)/cns-bt’ and ’Bowtie2’ represent the contiguity and quality of the respective contigs. Also E. coli K12 genome is denoted by ’ref’ and the consensus sequence constructed by Bowtie2 on E. coli genome is denoted by ’cns-bt’