From: A comprehensive evaluation of assembly scaffolding tools
Scaffolder | Read mapper | 10Â kb contigsa | 3Â kb contigs | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
 |  | Short fragment reads | Long fragment reads | Short fragment reads | Long fragment reads | ||||||
 |  | % Correct joins found | Score | % Correct joins found | Score | % Correct joins found | % Joins incorrect | Score | % Correct joins found | % Joins incorrect | Score |
ABySS | abyss-map | 100.0 | 1.00 | 66.7 | 0.91 | 98.9 | 0.0 | 1.00 | 99.5 | 0.0 | 1.00 |
Bambus2 | Bowtie 2 | 100.0 | 1.00 | 66.7 | 0.91 | 63.7 | 0.0 | 0.84 | 95.9 | 0.0 | 0.99 |
BWA | 48.2 | 0.82 | 48.2 | 0.87 | 59.6 | 0.0 | 0.82 | 96.2 | 0.0 | 0.99 | |
MIP | Bowtie -v 0 | 100.0 | 1.00 | 96.3 | 0.99 | 98.9 | 0.0 | 1.00 | 98.4 | 0.0 | 1.00 |
Bowtie -v 3 | 100.0 | 1.00 | 96.3 | 0.99 | 98.4 | 0.0 | 0.99 | 97.9 | 0.0 | 1.00 | |
Bowtie 2 | 100.0 | 1.00 | 29.6 | 0.82 | 96.3 | 0.5 | 0.74 | 98.7 | 0.5 | 0.96 | |
BWA | 100.0 | 1.00 | 33.3 | 0.83 | 98.0 | 1.1 | 0.54 | 98.2 | 0.4 | 0.96 | |
Opera | Bowtie | 100.0 | 1.00 | 92.6 | 0.98 | 98.4 | 0.0 | 0.99 | 1.0 | 10.0 | 0.79 |
BWA | 100.0 | 1.00 | 92.6 | 0.98 | 99.8 | 0.2 | 0.93 | 1.2 | 80.0 | 0.37 | |
SCARPA | Bowtie -v 0 | 100.0 | 1.00 | 96.3 | 0.99 | 98.9 | 0.0 | 1.00 | 95.0 | 0.0 | 0.99 |
Bowtie -v 3 | 100.0 | 1.00 | 96.3 | 0.99 | 98.6 | 0.0 | 0.99 | 96.3 | 0.0 | 0.99 | |
Bowtie 2 | 85.2 | 0.95 | 96.3 | 0.99 | 96.8 | 0.0 | 0.99 | 76.3 | 0.7 | 0.92 | |
BWA | 85.2 | 0.95 | 92.6 | 0.98 | 96.6 | 0.0 | 0.98 | 77.9 | 0.4 | 0.93 | |
SGA | Bowtie 2 | 100.0 | 1.00 | 96.3 | 0.99 | 97.3 | 0.0 | 0.99 | 97.6 | 0.0 | 1.00 |
BWA | 100.0 | 1.00 | 92.6 | 0.98 | 99.0 | 0.0 | 1.00 | 96.2 | 0.0 | 0.99 | |
SOAP2 | SOAP2 | 96.3 | 0.99 | 96.3 | 0.99 | 98.6 | 0.0 | 0.99 | 99.5 | 0.0 | 1.00 |
SOPRA | Bowtie -v 0 | 100.0 | 1.00 | 96.3 | 0.99 | 98.3 | 0.0 | 0.99 | 98.2 | 0.0 | 1.00 |
Bowtie -v 3 | 100.0 | 1.00 | 96.3 | 0.99 | 97.2 | 0.0 | 0.99 | 97.2 | 0.0 | 1.00 | |
Bowtie 2 | 74.1 | 0.91 | 100.0 | 1.00 | 91.5 | 0.5 | 0.82 | 85.6 | 0.5 | 0.93 | |
BWA | 74.1 | 0.91 | 88.9 | 0.97 | 92.9 | 0.2 | 0.89 | 83.1 | 0.4 | 0.93 | |
SSPACE | Bowtie -v 0 | 100.0 | 1.00 | 92.6 | 0.98 | 99.1 | 0.0 | 1.00 | 99.6 | 0.0 | 1.00 |
 | Bowtie -v 3 | 100.0 | 1.00 | 92.6 | 0.98 | 98.7 | 0.0 | 0.99 | 99.3 | 0.0 | 1.00 |