Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data

Ayelet Peres, Vered Klein, Boaz Frankel, William Lees, Pazit Polak, Mark Meehan, Artur Rocha, João Correia Lopes, Gur Yaari

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article numberbbae221
JournalBriefings in Bioinformatics
Volume25
Issue number3
DOIs
StatePublished - 27 Mar 2024

Bibliographical note

Publisher Copyright:
© 2024 The Author(s). Published by Oxford University Press.

Keywords

  • AIRR-seq
  • FAIR
  • annotation
  • pipelines
  • preprocessing
  • reproducibility

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