Fig. 1

Cross-validation of fixed-binning and HIFI methodologies. a Schematic representation of cross-validation methodology to assess the accuracy of fixed-binning and proposed HIFI methodologies. b Cross-validation error for canonical fixed-binning approaches, for different bin sizes, as a function of coverage, see also Additional file 1: Figure S1 for similar analyses of RF fixed binning, HIFI-KDE, and HIFI-AKDE. c Analysis of canonical fixed-binning error (relative to error with one RF per bin) across genomic distance between RF-pairs. No singular bin size performs best for all genomic distances. d Comparison of errors for different approaches. For fixed binning and HIFI-KDE, the optimal bin size or bandwidth was chosen separately for each coverage level. Nonetheless, HIFI-MRF outperforms all other approaches. e Comparison of errors (relative to error obtained with fixed binning using two RFs per bin) by genomic distance of RF pairs, using as input a set of 304M read pairs (50% of total training set). HIFI-MRF performs best across all distances