nf-core pipeline · dna, hla, hla-typing
nf-core/hlatyping
Precision human leukocyte antigen typing from next-generation sequencing data for DNA and RNA samples.
What nf-core/hlatyping is
nf-core/hlatyping is a bioinformatics workflow designed to carry out Human Leukocyte Antigen (HLA) genotyping from next-generation sequencing data. Originally developed by Christopher Mohr, Alexander Peltzer and Sven Fillinger, the pipeline automates the identification and characterisation of major histocompatibility complex (MHC) alleles from sequencing experiments.
Accurate HLA characterisation is vital for immunology, personalised medicine, and transplant compatibility assessments. The workflow accepts DNA or RNA data from whole genome, whole exome, and transcriptome sequencing experiments, generating 4-digit HLA class I predictions and supporting optional extended profiling of class I and class II loci.
What the pipeline does
The workflow begins by merging FASTQ files if required and running FastQC to examine raw sequencing read quality. Reads are indexed and mapped against a reference database of known MHC class I alleles using the Yara aligner.
Genotype calling is performed by OptiType, which uses an integer linear programming algorithm that considers all major and minor HLA-I loci simultaneously to identify the allele combination that explains the maximum number of aligned reads. Users can optionally run HLA-HD to predict both HLA class I and class II alleles, provided HLA-HD is installed locally. Read quality metrics across all samples are subsequently gathered into an aggregated report with MultiQC.
Key facts
- Workflow engine
- Nextflow DSL2
- Primary typing tool
- OptiType
- Optional typing tool
- HLA-HD
- Read aligner
- Yara
- Quality control tools
- FastQC, MultiQC
- Input formats
- FASTQ (single-end or paired-end), BAM
- Sequencing types
- DNA, RNA (WGS, WES, RNA-seq)
- Latest release
- 2.2.0 (2026-02-02)
What you can use it for
- Genomic HLA class I typing
- Identify 4-digit HLA-I alleles from paired-end or single-end whole genome or whole exome DNA sequencing.
- Transcriptomic HLA profiling
- Determine HLA class I genotypes directly from RNA sequencing and whole transcriptome datasets.
- Combined class I and II genotyping
- Execute simultaneous HLA class I and class II typing across cohorts using an optional local installation of HLA-HD.
- Sequencing quality reporting
- Evaluate cohort-wide raw read quality and processing statistics through automated FastQC and MultiQC reports.
Run it here
The research agent runs nf-core/hlatyping with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Delivers 4-digit HLA class I genotyping by optimising across major and minor loci simultaneously with integer linear programming.
- Accommodates both DNA and RNA inputs across whole genome, exome, and transcriptome protocols.
- Ensures reproducible execution across environments using isolated Docker or Singularity containers per process.
Watch out for
- Predicting HLA class II alleles requires a local installation of the third-party tool HLA-HD.
- Providing input in BAM format still requires maintaining the FASTQ column structure in the samplesheet.
Questions
Can I run nf-core/hlatyping without my own cluster?
The research agent runs nf-core/hlatyping with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/hlatyping under?
MIT, like every nf-core pipeline.
Which sequencing protocols are supported?
The pipeline supports single-end and paired-end reads from whole genome, whole exome, and transcriptome sequencing for both DNA and RNA.
Can BAM files be used directly as pipeline input?
Yes, BAM file paths can be specified in an additional bam column in the samplesheet, though the standard FASTQ columns must remain present.
Does the workflow resolve HLA class II alleles?
By default, OptiType resolves only HLA class I alleles. Combined class I and class II typing requires enabling HLA-HD, which must be installed locally.
How does OptiType select the reported genotype?
OptiType maps reads to MHC class I references using Yara and solves an integer linear programming problem to identify the allele combination accounting for the greatest number of reads.
How to cite it
doi: 10.5281/zenodo.1401039
Written from nf-core/hlatyping's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.