Unphased assembly refers to the process of assembling genomic or transcriptomic sequences without considering the phase information of genetic variations, such as single nucleotide polymorphisms (SNPs) or insertions/deletions (indels). In unphased assembly, the different alleles at a given position are treated independently and are not assigned to specific haplotypes. This means that the assembly does not capture the haplotype information and only provides a consensus sequence.
Partially phased assembly refers to the process of assembling genomic or transcriptomic sequences while considering some level of haplotype information. In partially phased assembly, the different alleles at a given position are assigned to specific haplotypes based on the phase information obtained from sequencing data. This allows for the reconstruction of haplotypes and provides a more comprehensive view of genetic variations within a population.
It is important to note that fully phased assembly, where all alleles are assigned to specific haplotypes, is often more challenging and requires additional computational and experimental efforts. Partially phased assembly strikes a balance between capturing haplotype information and the complexity of the assembly process.
