Accurate typing of human leukocyte antigen (HLA) is essential for successful organ transplantation and HLA genes are heavily associated with various diseases. Widely used typing assays often involve a set of specially designed primers or probes requiring additional experiments. With the maturing of high-throughput sequencing (HTS) technologies, whole genome sequencing (WGS) as well as other HTS assays are becoming more accessible even in the clinical settings. We describe various computational methods capable of directly typing HLA genes using HTS data including Kourami, our HLA assembler. Kourami is the first HLA assembler capable of discovering novel alleles. Kourami assembles full-length sequences across the peptide-binding regions of HLA genes. Here, we focus on how a user would use Kourami on a new sample. We demonstrate the application by typing HLA alleles from a recently published WGS data with validated HLA types using Kourami.