Table 2 Approximate runtimes of the FAN-C matrix generation pipeline. Data from the GM12878 B-lymphocyte dataset [25]. Runtimes are normalised to a single thread, and expressed as minutes per 100 million read pairs. All processing performed on a Linux SGE cluster with AMD Opteron Processor 6376
Minutes/100 M read pairs (single thread) | |
|---|---|
Rao et al. [25] GM12878 | |
BWA mem, ligation junction split | 4061.95 |
Loading + mappability, quality, and uniqueness filters | 264.03 |
PCR duplicate, RE distance, ligation error filters | 224.15 |
Fragment-level assembly | 55.72 |
Merge | 91.09 |
Binning, low coverage filter, ICE correction, expected value calculation | |
1 Mb bins | 167.68 |
25 kb bins | 822.15 |
5 kb bins | 1455.1 |