Table 3.
Alignment results against experimental E.coli optical map
| Software | Total alignments | Contigs with alignment | Contigs with correct alignment | Contigs with unique alignment | Contigs with unique and correct alignment | Runtime |
|---|---|---|---|---|---|---|
| TWIN | 101 | 11 | 7 | 4 | 0 | 0.76s |
| (3.44 Mb) | (0.49 Mb) | (0.26 Mb) | (0.23 Mb) | (0.00 Mb) | ||
| SOMA | 6 | 6 | 0 | 6 | 0 | 14.45s |
| (0.25 Mb) | (0.25 Mb) | (0.00 Mb) | (0.25 Mb) | (0.00 Mb) | ||
| malignerIX | 81 | 15 | 13 | 7 | 5 | 0.15s |
| (3.23 Mb) | (0.99 Mb) | (0.87 Mb) | (0.65 Mb) | (0.53 Mb) | ||
| malignerDP | 208 | 28 | 26 | 13 | 13 | 0.31s |
| (8.35 Mb) | (2.37 Mb) | (2.24 Mb) | (1.60 Mb) | (1.60 Mb) |
Number of contigs (and bp) aligned to the experimental E.coli consensus optical map. A contig is considered to be placed correctly if its location given as percentage of optical map length is within 5% of the location reported by nucmer. Among these software, the only alignment method which is able to handle the experimental error characteristics of real data is malignerDP. Index-based methods, being less flexible, are not able to find the same number of correct placements.