Identifies allelic variation given a Whole Genome Shotgun (WGS) assembly of haploid sequences. Celera assembler is an algorithm to produce a set of haploid consensus sequences rather than a single consensus sequence. It uses a dynamic windowing approach and detects alleles by simultaneously processing the portions of aligned reads spanning a region of sequence variation. Celera assembler also assigns reads to their respective alleles, phases adjacent variant alleles and generates a consensus sequence corresponding to each confirmed allele.