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Purpose
A simple workflow to generate research-grade consensus sequences from high-throughput (next-generation) DNA sequencing of individual or multiplexed, clonally-amplified genes representing the major histocompatibility complex (MHC), including HLA-A, -B, -C, -DQB1, -DPB1, and -DRB1 as well as KIR.
NON-CLINICAL RESEARCH USE ONLY
The pipeline is designed to enable processing of targeted HLA NGS with the intent of further open source development to allow processing of additional genomic regions such as ABO/Rh, other targeted gene systems, whole-exomes or whole-genomes with paired or unpaired data from multiple sequencing platforms (Sanger, Illumina, Pacific Biosciences, Oxford Nanopore, Ion Torrent, or combinations thereof) and diverse applications (research, donor recruitment typing, clinical diagnostics, etc). Where specific parameters, filtering criteria, software or hardware configurations appear to overfit the pipeline to targeted HLA NGS the NMDP will document and disclose as release notes.
The pipeline represents what we consider to be a minimally viable workflow for generating consensus DNA sequence and interpretable alleles. Further details are provided below or you can get started with a tutorial.