Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer
news ·Our latest publication in Current Protocols presents a streamlined procedure for HLA prediction using streaming long-read sequence alignments.
Long-read platforms such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) now offer the accuracy and throughput needed to resolve highly polymorphic regions of the human genome, including the human leukocyte antigen (HLA) gene cluster—a key component of immune response. Our streamlined protocol enables direct streaming of sequence alignments into HLAminer, eliminating the need for large alignment files while maintaining high prediction accuracy. Tested on low-coverage (10×) whole-genome sequencing data, this method is computationally efficient and compatible with any aligner supporting the SAM file format.
This work enhances the accessibility and efficiency of HLA typing using third-generation sequencing, with implications for transplant matching, disease association studies, and immunogenetics research.