Table 1.
Comparison of Hi-C structural inference methods
| Name | Type | Results from 1-kbp-resolution data | Inter-chromosomal? |
|---|---|---|---|
| miniMDS | Optimization | Success | Yes |
| BACH | Modeling | Bug | No |
| ShRec3D | Optimization | Success | No |
| MOGEN (Trieu and Cheng, 2014) | Optimization | Exceeds maximum input size | No |
| 3D-GNOME (Szałaj et al., 2016) | Optimization | Success (graphical output only) | Yes |
| ChromSDE (Zhang et al., 2013) | Optimization | Failed to produce output in reasonable time | No |
| tRex (Park and Lin, 2016) | Modeling | Requires fragment length | No |
| MCMC5 (Rousseau et al., 2011) | Modeling | Requires standard deviation | No |
| PASTIS (Varoquaux et al., 2014) | Modeling | Failed to install IPOPT | Yes |
| TAD-bit (Baù and Marti-Renom, 2012) | Optimization | Failed to produce output in reasonable time | Yes |
| HSA (Zou et al., 2016) | Modeling | Memory error | No |
| Chromosome3D (Adhikari et al., 2016) | Optimization | Failed to produce output in reasonable time | No |
| InfMod3DGen (Wang et al., 2015) | Modeling | Bug (error was corrected while the current manuscript was in press) | No |