Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data
- PMID: 38752856
- PMCID: PMC11097599
- DOI: 10.1093/bib/bbae221
Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data
Abstract
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.
Keywords: AIRR-seq; FAIR; annotation; pipelines; preprocessing; reproducibility.
© The Author(s) 2024. Published by Oxford University Press.
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