A method of determining HLA type comprising: (a) selectively amplifying a nucleic acid molecule from an individual, said nucleic acid molecule comprising i. at least a portion of a first exon of an HLA gene; ii. at least a portion of a second exon of said HLA gene; and iii. the intron between said first and second exons, thereby generating an amplified exon pair; wherein the amplified exon pair comprises at least a portion of a first exon of an HLA gene, at least a portion of a second exon of an HLA gene and at least a portion of an intronic sequence spanning the two exons; (b) carrying out a sequencing read of a first region of the amplified exon pair, said first region comprising at least a portion of said first exon and a portion of the intron adjacent to said first exon; (c) carrying out a sequencing read of a second region of the amplified exon pair; said second region comprising at least a portion of said second exon and a portion of the intron adjacent to said second exon; (d) performing steps (b) and (c) a plurality of times to generate a plurality of paired sequencing reads of said HLA gene, said plurality of paired sequencing reads comprising sequence information from at least two different haplotypes; (e) partitioning each sequencing read into one of two different haplotypes, wherein said partitioning comprises: i. randomly selecting a first and second paired sequencing read and designating the reads as haplotype 1 and haplotype 2, respectively; ii. assigning each remaining paired sequencing read in said plurality of paired sequencing reads to said haplotype 1 or said haplotype 2 based on sequence similarity to either haplotype 1 or haplotype 2; iii. computing a consensus sequence for haplotype 1 and a consensus sequence for haplotype 2 using the paired sequence reads assigned to each haplotype; and iv. designating said consensus sequences as haplotypes 1 and 2 and repeating steps (i) - (iv) until said consensus sequences no longer change; and (f) determining the HLA type of said individual based on said partitioned sequencing reads; wherein said first exon is exon 2 of said HLA gene and/or said second exon is exon 3 of said HLA gene; and wherein said HLA gene is selected from the group consisting of: HLA-A, HLA-B and HLA-C. (a) selectively amplifying a nucleic acid molecule from an individual, said nucleic acid molecule comprising i. at least a portion of a first exon of an HLA gene; ii. at least a portion of a second exon of said HLA gene; and iii. the intron between said first and second exons, thereby generating an amplified exon pair; wherein the amplified exon pair comprises at least a portion of a first exon of an HLA gene, at least a portion of a second exon of an HLA gene and at least a portion of an intronic sequence spanning the two exons; i. at least a portion of a first exon of an HLA gene; ii. at least a portion of a second exon of said HLA gene; and iii. the intron between said first and second exons, thereby generating an amplified exon pair; wherein the amplified exon pair comprises at least a portion of a first exon of an HLA gene, at least a portion of a second exon of an HLA gene and at least a portion of an intronic sequence spanning the two exons; (b) carrying out a sequencing read of a first region of the amplified exon pair, said first region comprising at least a portion of said first exon and a portion of the intron adjacent to said first exon; (c) carrying out a sequencing read of a second region of the amplified exon pair; said second region comprising at least a portion of said second exon and a portion of the intron adjacent to said second exon; (d) performing steps (b) and (c) a plurality of times to generate a plurality of paired sequencing reads of said HLA gene, said plurality of paired sequencing reads comprising sequence information from at least two different haplotypes; (e) partitioning each sequencing read into one of two different haplotypes, wherein said partitioning comprises: i. randomly selecting a first and second paired sequencing read and designating the reads as haplotype 1 and haplotype 2, respectively; ii. assigning each remaining paired sequencing read in said plurality of paired sequencing reads to said haplotype 1 or said haplotype 2 based on sequence similarity to either haplotype 1 or haplotype 2; iii. computing a consensus sequence for haplotype 1 and a consensus sequence for haplotype 2 using the paired sequence reads assigned to each haplotype; and iv. designating said consensus sequences as haplotypes 1 and 2 and repeating steps (i) - (iv) until said consensus sequences no longer change; and i. randomly selecting a first and second paired sequencing read and designating the reads as haplotype 1 and haplotype 2, respectively; ii. assigning each remaining paired sequencing read in said plurality of paired sequencing reads to said haplotype 1 or said haplotype 2 based on sequence similarity to either haplotype 1 or haplotype 2; iii. computing a consensus sequence for haplotype 1 and a consensus sequence for haplotype 2 using the paired sequence reads assigned to each haplotype; and iv. designating said consensus sequences as haplotypes 1 and 2 and repeating steps (i) - (iv) until said consensus sequences no longer change; and (f) determining the HLA type of said individual based on said partitioned sequencing reads;