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Additional file 1: Figure S1. Haplotype structures of the zebra finch assemblies for all chromosomes. Figure S2. Hap-mer blob plots for budgerigar data. Figure S3. Hap-mer blob plots for black rhinoceros data. Figure S4. Hap-mer blob plots for sterlet data. Figure S5. Merge haplotype step. Figure S6. Consensus scaffolding using long reads. Figure S7. Consensus scaffolding using Hi-C. Figure S8. Detection of erroneous edges using Hi-C. Figure S9. Detection of misassembly using Hi-C. Figure S10. Detection of erroneous edges using long reads. Figure S11. Phasing steps. Figure S12. Execution of FALCON-Phase and Hi-C scaffolding tools. Table S1. Sample information. Table S2. Contig assembly statistics. Table S3. Knock-out test for evaluation of the characteristic functions of GreenHill. Table S4. Resource requirements.