Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data

• Type: Article in International Scientific Journal
• Date: 2024

Authors

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

Journal

Title: Briefings in Bioinformatics

Vol. 25

ISSN: 1467-5463

Publisher: Oxford University Press

Indexing

ISI Web of Knowledge - 0 Citations

Scopus - 0 Citations

Other information

Authenticus ID: 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8