1. nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.
- Author
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Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen CG, Ladd D, Polster M, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, and Kleinstein SH
- Subjects
- Humans, Receptors, Antigen, B-Cell genetics, Receptors, Antigen, B-Cell immunology, Software, Single-Cell Analysis methods, High-Throughput Nucleotide Sequencing methods, Adaptive Immunity genetics, B-Lymphocytes immunology, T-Lymphocytes immunology, Workflow, COVID-19 immunology, COVID-19 virology, COVID-19 genetics, SARS-CoV-2 immunology, SARS-CoV-2 genetics, Receptors, Antigen, T-Cell genetics, Receptors, Antigen, T-Cell immunology, Computational Biology methods
- Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: SHK receives consulting fees from Peraton. AP is an employee of Boehringer Ingelheim Pharma GmbH & Co KG and declares no conflict of interest. DL is an employee of oNKo-innate Pty Ltd and declares no conflict of interest. MCK has served on advisory boards and received speaker fees / travel grants from Merck, Sanofi-Genzyme, Novartis, Biogen, Janssen, Alexion, Celgene / Bristol-Myers Squibb and Roche. He has received research grants from Merck, Roche, Novartis, Sanofi-Genzyme and Celgene / Bristol-Myers Squibb. All other authors declare no conflicts of interest., (Copyright: © 2024 Gabernet et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2024
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