nf-core pipeline ·
nf-core/abotyper
A bioinformatics pipeline to determine ABO blood group phenotypes from long-read sequencing data.
What nf-core/abotyper is
nf-core/abotyper is a bioinformatics pipeline designed to deduce human ABO blood group phenotypes and red cell antigens from third-generation sequencing data of the ABO gene (alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase). Originally developed by Fredrick M. Mobegi at the Department of Clinical Immunology, PathWest Laboratory Medicine WA, it was built specifically to automate the analysis of amplicon sequencing assays focusing on key coding regions.
Conventional serological blood typing can be augmented or clarified through genetic analysis, particularly by interrogating clinically relevant polymorphisms. The pipeline standardises the analysis workflow by taking FASTQ sequencing files and a samplesheet, aligning reads against a calibrated reference gene, identifying single-nucleotide variants, phasing alleles into haplotypes, and predicting final ABO blood group phenotypes alongside comprehensive alignment and quality metrics.
What the pipeline does
The workflow begins by running FastQC to assess raw read quality from input FASTQ files. Reads are aligned against a single combined reference sequence, the ABO RefSeqGene NG_006669.2 (spanning exons 2 to 7), using Minimap2. Samtools then computes alignment coverage, flagstat metrics, and detailed mapping statistics. Following alignment, Clair3 performs small variant calling and phasing directly from the BAM files.
Custom local modules process Clair3's gVCF and phased VCF outputs: ABO_CLAIR2METRICS and ABO_CLAIR2HAPLOTYPES convert variant calls into per-position allele frequencies and read-equivalent haplotypes. The ABO_GETABOSNPS module extracts ABO-relevant single-nucleotide variants using coordinate calibration and marker positions defined in a variant panel YAML file (derived from NCBI RefSeq and dbRBC databases). The ABO_SNPS2PHENO module combines the identified SNP and haplotype patterns to deduce the ABO phenotype. Finally, MultiQC collates alignment, variant, and quality control metrics into an aggregated report.
Key facts
- Pipeline engine
- Nextflow (nf-core)
- Original developer
- Fredrick M. Mobegi (Department of Clinical Immunology, PathWest Laboratory Medicine WA)
- Primary sequencing technology
- Oxford Nanopore Technologies (MinION)
- Input formats
- FASTQ, CSV (samplesheet)
- Output formats
- BAM, BAI, TSV, TXT, CSV, XLSX, HTML
- Reference sequence
- NCBI RefSeqGene NG_006669.2 (LRG_792, exons 2–7)
- Core aligner
- Minimap2 (v2.30)
- Variant caller
- Clair3 (v2.0.0)
What you can use it for
- Nanopore ABO amplicon typing
- Deduce human ABO blood group phenotypes from barcoded Oxford Nanopore MinION amplicon sequencing targeting ABO exons 6 and 7.
- ABO single-nucleotide variant profiling
- Identify, phase, and quantify allele frequencies for known ABO-associated single-nucleotide variants across clinical sequencing cohorts.
- Haplotype-based phenotype prediction
- Reconstruct per-read-equivalent haplotypes from phased variants to resolve complex ABO blood group alleles and produce structured Excel summaries.
Run it here
The research agent runs nf-core/abotyper 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
- Provides an end-to-end automated workflow from raw Oxford Nanopore reads to variant calling, phasing, and blood group phenotype deduction.
- Aligns to a single unified reference sequence (NG_006669.2) calibrated against dbRBC and NCBI RefSeq databases.
- Produces both summary spreadsheets (CSV and Excel) and detailed per-sample alignment metrics, BAM files, and haplotype reports.
- Supports multiple containerisation and environment solutions including Conda, Docker, and Singularity profiles.
Watch out for
- Sequencing reads must span the ABO exon 6 and exon 7 regions for accurate blood group determination.
- Input FASTQ files require specific barcode-based naming structures matching a defined regular expression, or the pipeline falls back to a default barcode assignment.
- Compatibility with PacBio, Ion Torrent, and Illumina platforms is still undergoing testing.
Questions
Can I run nf-core/abotyper without my own cluster?
The research agent runs nf-core/abotyper 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/abotyper under?
MIT, like every nf-core pipeline.
Which genomic regions must be covered by the sequencing assay?
Sequencing reads must span ABO exons 6 and 7 within the combined NG_006669.2 reference sequence, as these contain the primary polymorphisms required for ABO blood group determination.
Can data from sequencing platforms other than Oxford Nanopore be analysed?
While originally developed and validated for Oxford Nanopore MinION data, the pipeline can handle FASTQ files from PacBio, Ion Torrent, and Illumina platforms, though these are currently undergoing testing.
What naming convention is expected for input FASTQ files?
Filenames must end with '_barcode' followed by digits to denote the barcode index (for example, 'Sample1-2024-12345_barcode22.fastq'). Files without the expected structure will fall back to 'barcode00'.
What files contain the final predicted blood group results?
Results are summarised at the project level in 'final_export.csv' and 'ABO_result.xlsx', with per-sample details provided in 'SAMPLE.ABOPhenotype.txt' and 'SAMPLE.Haplotypes.tsv'.
How to cite it
Fredrick M. Mobegi, Samuel Bruce, Naser El-Lagta, Felipe Ayora, Benedict M. Matern, Mathijs Groeneweg, Lloyd J. D'Orsogna & Dianne De Santis. Characterisation of the ABO Blood Group Phenotypes Using Third-Generation Sequencing. Int. J. Mol. Sci. 2025 Jun 06. doi: 10.3390/ijms26125443.
Written from nf-core/abotyper's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.