Fig. 1: Overview of the PhaseGrass workflow with red, green and purple rectangles indicating input data, computational tools and output results of the workflow, respectively.

PhaseGrass includes the following steps (dashed frames): (1), initial primary contig assembly with either ONT or PacBio HiFi data; (2), generating a chromosome-level, unphased haploid assembly; (3), reference-based phasing; (4), partitioning long reads or unitigs (from step 1) to haplotype-specific sets; (5), assembling each set of binned ONT reads independently and polishing of the resulting contigs. This step is only intended for ONT reads; (6), generating the final chromosome-level haplotype-resolved diploid assembly.