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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

From: FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

  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