Haplotypes provide a better picture of the genome as compared to genotype as they include information about the presence of the particular allele on a chromosome. Haplotyping is a challenging task because the standard methods for genotyping only provide information about the individual's alleles at the specific genetic locus and not across the full lengh of a gene. In addition, the existing methods either very slow for routine applications as they traditionally require analyzing the polymorphic markers in pedigree members for humans or experiments studying segregation of alleles in other organism. With the advancement in sequencing technologies, a plathora of draft genomes has become available in recent years requiring a better approach to haplotyping. In this project, we propose to develop a method that uses next-generation sequencing data for haplotyping. By systematically analyzing the heterozygous positions along the sequencing reads, haplotypes can be accurately assigned across the full length of a gene. We will use the newly develop method to assign haplotypes in the mango transcriptome.