Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data

• Tipo: Artigo em Revista Científica Internacional
• Data: 2024

Autores

Peres, A (Autor) Outra; Klein, V (Autor) Outra; Frankel, B (Autor) Outra; Lees, W (Autor) Outra; Polak, P (Autor) Outra; Meehan, M (Autor) Outra; Rocha, A (Autor) Outra; João Correia Lopes (Autor) FEUP; Yaari, G (Autor) Outra

Revista

Título: Briefings in Bioinformatics

Vol. 25

ISSN: 1467-5463

Editora: Oxford University Press

Indexação

ISI Web of Knowledge - 0 Citações

Scopus - 0 Citações

Outras Informações

ID Authenticus: P-010-ECV

DOI: 10.1093/bib/bbae221

Abstract (EN): 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.

Idioma: Inglês

Tipo (Avaliação Docente): Científica

Nº de páginas: 8