| Â | Â | Â | Â | Placed finishing reads | Gaps closed |
|---|
Species
|
Candidate gaps
|
# Bounds
|
# Finishing reads
|
Control
|
Bounded
|
Alternate
|
Control
|
Bounded
|
Alternate
|
E. coli O157:H7 | 14 (1) | 56 | 128 | 26 | 92 | N/A | 0 | 11 | N/A |
S. enterica
| 2 (0) | 18 | 33 | 14 | 23 | N/A | 0 | 1 | N/A |
B. mallei
| 9 (0) | 23 | 40 | 4 | 27 | N/A | 0 | 4 | N/A |
I. multifiliis
| 11 (2) | 14 | 21 | 3 | 21 | 17 | 0 | 6 | 4 |
E. coli K12 | 49 (2) | 23 | 60 | 12 | 49 | 11 | 0 | 29 | 0 |
C. amycolatum
| 4 (0) | 3 | 3 | 0 | 2 | 0 | 0 | 1 | 0 |
Total | 89 (5) | 137 | 285 | 59 | 214 | 28 | 0 | 52 | 4 |
- Comparison of three algorithms. Control uses finishing reads like WGS reads. Bounded uses finishing reads with placement constraints. Alternate uses finishing reads in a second round of assembly without constraints. Candidate gaps include both regions in the control assembly between finishing constraints with zero coverage and a consensus sequence derived from a repeat unitig or no consensus sequence in the control assembly. The parentheses indicate the number of gaps with no consensus sequence in the control assembly. The gap and spanning constraint are not necessarily 1-to-1. Bounds: The total number of bounding constraints that span the repeat gap or were not satisfied in both control and bounded assemblies. Finishing reads: The total number of finishing reads generated for the bounds in the table. Placed finishing reads: The total number of finishing reads placed in the assembly by each of the assembly algorithms. Gaps closed: The number of gaps closed by filling in missing consensus sequence or by tiling repeat instances with reads. By definition, the control assembly always closes 0 gaps. The bounded assembly joins were verified by alignment to finished reference, where available.
