Fig. 1

HLAscan workflow. The algorithm of HLAscan is explained schematically in five main steps. Step 1 depicts collection of read sequences of HLA genes produced from a sample. Step 2 demonstrates alignment of HLA-A gene read sequence to the human reference genome sequence. In step 3, HLA-A read sequences are aligned to specific allele types. From the candidate alleles, true allele types are determined by applying a score function (step 3 to step 4) and resolving phasing issues (step 4 to step 5). Gray vertical lines under reference sequences represent positions with sequence variance. Black arrows in alleles A*02, A*03, and A*05 of step 3 indicate genetic positions with no sequence reads aligned. Circled bases in step 4, A and T in A*01, and T in A*04 represent unique sequences that are not redundant with base sequences in any other ranked alleles