A method for diploid genome assembly and haplotype sequence reconstruction, the method performed by at least one software component executing on a processor, the method comprising: generating a fused assembly graph from reads of both haplotypes, the fused assembly graph including identified primary contigs and associated contigs; generating haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads; merging the fused assembly graph and haplotype-specific assembly graphs to generate a merged assembly haplotype graph; removing cross-phasing edges from the merged assembly haplotype graph to generate a final haplotype-resolved assembly graph; and reconstructing haplotype-specific contigs from the final haplotype-resolved assembly graph resulting in haplotype-specific contigs; wherein generating the haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads, further comprises: for each haplotype-fused contig of haplotype-fused contigs, identifying a subset of raw reads that belong to that haplotype-fused contig; phasing the reads to sort the reads into groups representing different haplotypes using single nucleotide polymorphism information; and unzipping the haplotype-fused contigs to haplotype-specific contigs; wherein for each haplotype-fused contig of haplotype-fused contigs, identifying a subset of raw reads that belong to that haplotype-fused contig further comprises: collecting the reads originating from the same genomic region of a contig using the overlapping data for generating the assembly; and phasing the reads from the same contig by block and phase. generating a fused assembly graph from reads of both haplotypes, the fused assembly graph including identified primary contigs and associated contigs; generating haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads; merging the fused assembly graph and haplotype-specific assembly graphs to generate a merged assembly haplotype graph; removing cross-phasing edges from the merged assembly haplotype graph to generate a final haplotype-resolved assembly graph; and reconstructing haplotype-specific contigs from the final haplotype-resolved assembly graph resulting in haplotype-specific contigs; wherein generating the haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads, further comprises: for each haplotype-fused contig of haplotype-fused contigs, identifying a subset of raw reads that belong to that haplotype-fused contig; phasing the reads to sort the reads into groups representing different haplotypes using single nucleotide polymorphism information; and unzipping the haplotype-fused contigs to haplotype-specific contigs; wherein for each haplotype-fused contig of haplotype-fused contigs, identifying a subset of raw reads that belong to that haplotype-fused contig further comprises: collecting the reads originating from the same genomic region of a contig using the overlapping data for generating the assembly; and phasing the reads from the same contig by block and phase. for each haplotype-fused contig of haplotype-fused contigs, identifying a subset of raw reads that belong to that haplotype-fused contig; phasing the reads to sort the reads into groups representing different haplotypes using single nucleotide polymorphism information; and unzipping the haplotype-fused contigs to haplotype-specific contigs; wherein for each haplotype-fused contig of haplotype-fused contigs, identifying a subset of raw reads that belong to that haplotype-fused contig further comprises: collecting the reads originating from the same genomic region of a contig using the overlapping data for generating the assembly; and phasing the reads from the same contig by block and phase. collecting the reads originating from the same genomic region of a contig using the overlapping data for generating the assembly; and phasing the reads from the same contig by block and phase.