Table 1.
Comparison of different software tools for fragment assembly
| ideal | euler | phrap | cap3 | tigr assembler | ||
|---|---|---|---|---|---|---|
| CJ | No. of contigs (no. of misassembled contigs) | 24 (5) | 29 (0) | 33 (2) | 54 (3) | >300 (>10) |
| Coverage by contigs | 99.5% | 96.7% | 94.0% | 92.4% | 90.0% | |
| Coverage by misassembled contigs | – | 0.0% | 16.1% | 13.6% | 1.2% | |
| NM | No. of contigs (no. of misassembled contigs) | 79 (126) | 149 (0) | 160 (17) | 163 (14) | >300 (9) |
| Coverage by the contigs | 99.8% | 99.1% | 98.6% | 97.2% | 87.4% | |
| Coverage by misassembled contigs | – | 0.0% | 10.5% | 9.2% | 1.3% | |
| LL | No. of contigs (no. of misassembled contigs) | 6 (61) | 58 (0) | 62 (10) | 85 (8) | 245 (2) |
| Coverage by the contigs | 99.9% | 99.5% | 97.6% | 97.0% | 90.4% | |
| Coverage by misassembled contigs | – | 0.0% | 19.0% | 11.4% | 0.7% |
ideal is an imaginary assembler that outputs the collection of islands in clone coverage as contigs. In the ideal column, the number in parentheses shows the overall multiplicity of tangles. CJ, NM, and LL correspond to the Campylobacter jejuni (12), Neisseria meningitidis (NM) (13), and Lactococcus lactis (14) sequencing projects.