Fig. 1

Overview of the GCphase workflow. a Data preprocessing. GCphase simplifies the reads into a format that contains only SNP information. b Selecting SNPs and long reads. SNP loci with disproportionately large allele ratios (the number of reads supporting the major allele accounts for more than 85% of the total number of reads) and reads with insufficient SNP information (indicated by red borders in the graph) were removed. c Constructing the Graph. The two alleles of SNP loci are represented as vertices in the graph, and the reads supporting two alleles are represented as edges. d Partitioning Graph. The graph is partitioned into two sets with the smallest intersection using the minimum-cut algorithm. e Correcting errors and Producing haplotype blocks. After undergoing two error correction steps, the algorithm traverses the maximal connected components in the graph to generate haplotype blocks as the output