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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.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012265","type":"journal-article","created":{"date-parts":[[2024,7,26]],"date-time":"2024-07-26T13:48:45Z","timestamp":1722001725000},"page":"e1012265","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["nf-core\/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7049-9474","authenticated-orcid":true,"given":"Gisela","family":"Gabernet","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanna","family":"Marquez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Bjornson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Peltzer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailong","family":"Meng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8683-4772","authenticated-orcid":true,"given":"Edel","family":"Aron","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noah Y.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cole G.","family":"Jensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Ladd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Polster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Friederike","family":"Hanssen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Heumos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"nf-core community","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gur","family":"Yaari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus C.","family":"Kowarik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Nahnsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven H.","family":"Kleinstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,7,26]]},"reference":[{"issue":"6","key":"pcbi.1012265.ref001","article-title":"V(D)J Recombination: Mechanism, Errors, and Fidelity","volume":"2","author":"DB Roth","year":"2014","journal-title":"Microbiol Spectr"},{"issue":"5909","key":"pcbi.1012265.ref002","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/302575a0","article-title":"Somatic generation of antibody diversity","volume":"302","author":"S. 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Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"issue":"4","key":"pcbi.1012265.ref067","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","article-title":"phangorn: phylogenetic analysis in R","volume":"27","author":"KP Schliep","year":"2011","journal-title":"Bioinformatics"},{"issue":"11","key":"pcbi.1012265.ref068","doi-asserted-by":"crossref","first-page":"3594","DOI":"10.1093\/bioinformatics\/btaa158","article-title":"immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking","volume":"36","author":"CR Weber","year":"2020","journal-title":"Bioinformatics"},{"key":"pcbi.1012265.ref069","doi-asserted-by":"crossref","first-page":"1133967","DOI":"10.3389\/fimmu.2023.1133967","article-title":"Cladribine treatment specifically affects peripheral blood memory B cell clones and clonal expansion in multiple sclerosis patients","volume":"14","author":"C Ruschil","year":"2023","journal-title":"Front Immunol"},{"issue":"12","key":"pcbi.1012265.ref070","doi-asserted-by":"crossref","first-page":"e94","DOI":"10.1093\/nar\/gks251","article-title":"Grinder: a versatile amplicon and shotgun sequence simulator","volume":"40","author":"FE Angly","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pcbi.1012265.ref071","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/s12859-016-0976-y","article-title":"Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data","volume":"17","author":"M Schirmer","year":"2016","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pcbi.1012265.ref072","doi-asserted-by":"crossref","first-page":"lqab019","DOI":"10.1093\/nargab\/lqab019","article-title":"Sequencing error profiles of Illumina sequencing instruments","volume":"3","author":"N Stoler","year":"2021","journal-title":"NAR Genomics Bioinforma"},{"issue":"2","key":"pcbi.1012265.ref073","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.immuni.2020.06.024","article-title":"Next-Generation Sequencing of T and B Cell Receptor Repertoires from COVID-19 Patients Showed Signatures Associated with Severity of Disease","volume":"53","author":"C Schulthei\u00df","year":"2020","journal-title":"Immunity"},{"issue":"4","key":"pcbi.1012265.ref074","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/j.chom.2020.09.002","article-title":"Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2","volume":"28","author":"SCA Nielsen","year":"2020","journal-title":"Cell Host Microbe"},{"key":"pcbi.1012265.ref075","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/s41421-020-0168-9","article-title":"Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing","volume":"6","author":"W Wen","year":"2020","journal-title":"Cell Discov"},{"issue":"11","key":"pcbi.1012265.ref076","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1038\/s42256-021-00413-z","article-title":"The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires","volume":"3","author":"M Pavlovi\u0107","year":"2021","journal-title":"Nat Mach Intell"},{"issue":"17","key":"pcbi.1012265.ref077","doi-asserted-by":"crossref","first-page":"4230","DOI":"10.1093\/bioinformatics\/btac505","article-title":"CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching","volume":"38","author":"T Rognes","year":"2022","journal-title":"Bioinforma Oxf Engl"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1012265","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012265","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T13:48:08Z","timestamp":1723038488000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012265"}},"subtitle":[],"editor":[{"given":"Anna","family":"Niarakis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,7,26]]},"references-count":77,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2024,7,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1012265","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.01.18.576147","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,26]]}}}