Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.
Brief Bioinform
; 25(3)2024 Mar 27.
Article
de En
| MEDLINE
| ID: mdl-38752856
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.
Mots clés
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Logiciel
/
Biologie informatique
Limites:
Humans
Langue:
En
Journal:
Brief Bioinform
Sujet du journal:
BIOLOGIA
/
INFORMATICA MEDICA
Année:
2024
Type de document:
Article
Pays d'affiliation:
Israël