查看文章

NeXtype is a software aiming at high-accuracy HLA typing based on short amplicon Next Generation Sequencing (NGS) data from Illumina MiSeq systems.

NeXtype employs advanced statistical algorithms that use high number of reads and associated Q-values delivered by NGS. In our NGS setup, MiSeq provides raw sequence data of paired-end reads. For all samples, 6 loci are considered on exons 2 and 3. The neXtype workflow is organized in several consecutive steps. Up-front, pre-run data is assembled, including a tree-structured HLA library and primer information. In the first step of an individual typing run, the primer sequence is identified for each read by a multi-level process that involves direct string comparison and also adapts to sequencing errors. Next, for each pair of reads the most likely matches in the HLA library are determined using Q-values and the predefined tree structure. The third …