Table 1 Rhodobacter sphaeroides 2.4.1 assembly evaluation
From: De novo likelihood-based measures for comparing genome assemblies
Contigs | Scaffolds | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Assembler | LAP | LAP | N50 (kb) | CN50 (kb) | LAP reads | LAP mates | N50 (kb) | CN50 (kb) | Unaligned | Unaligned |
reads | mates | reads | mates | |||||||
(fraction) | (fraction) | |||||||||
ABySS | -20.924 | -27.365 | 5.9 | 4.2 | -20.929 | -27.320 | 9 | 5 | 0.228 | 0.524 |
Allpaths-LG | -20.795 | -27.141 | 42.5 | 34.4 | -20.796 | -27.099 | 3,192 | 3,192 | 0.212 | 0.441 |
Bambus2 | -21.528 | -27.439 | 93.2 | 12.8 | -21.531 | -27.424 | 2,439 | 2,419 | 0.270 | 0.501 |
CABOG | -22.550 | -27.749 | 20.2 | 17.9 | -22.550 | -27.714 | 66 | 55 | 0.345 | 0.540 |
MSR-CA | -21.496 | -27.407 | 22.1 | 19.1 | -21.497 | -27.324 | 2,976 | 2,966 | 0.268 | 0.478 |
SGA | -20.896 | -27.575 | 4.5 | 2.9 | -21.030 | -27.416 | 51 | 51 | 0.237 | 0.541 |
SOAPdenovo | -20.816 | -27.160 | 131.7 | 14.3 | -20.816 | -27.152 | 660 | 660 | 0.214 | 0.453 |
Velvet | -20.903 | -27.314 | 15.7 | 14.5 | -20.907 | -27.246 | 353 | 270 | 0.219 | 0.471 |
R. sphaeroides ATCC 17025 | -29.391 | -29.973 | 3,218 | 3,218 | -29.391 | -29.973 | 3,218 | 3,218 | 0.813 | 0.904 |
R. capsulatus | -29.953 | -29.997 | 3,739 | 3,739 | -29.953 | -29.997 | 3,739 | 3,739 | 0.978 | 0.995 |
truth | -20.769 | -27.071 | 3,189 | 3,189 | -20.769 | -27.071 | 3,189 | 3,189 | 0.209 | 0.432 |