kTypeR – accurate and efficient alignment-free HLA genotyping using nanopore sequencing
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Attempts to leverage nanopore sequence data for HLA genotyping are rapidly gaining traction in the HLA community as the technology promises easy and costeffective library preparation and reads that cover the full extent of HLA Class I and Class II genes. Current typing strategies using nanopore sequences all rely on classical alignment-based methods. Due to the high per-read error-rates of nanopore reads, these algorithms typically perform considerably less robustly than when applied to short-reads. Here, we present ktypeR, which uses a fundamentally different strategy for genotyping. KtypeR compares all k-mers of each individual read to the pre-processed IPD-IMGT/HLA database and infers the most likely true alleles by majority vote.