SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.

Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

Publication: Oxford : Oxford University Press
Original Publication: London ; Birmingham, AL : H. Stewart Publications, [2000-

Computational Biology*/methods ; DNA Copy Number Variations* ; Software*; Humans ; Whole Genome Sequencing/methods ; Reproducibility of Results ; Workflow

Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner. SAMURAI is built using established community standards, ensuring portability, scalability, and reproducibility. The pipeline features a modular design with independent blocks for data preprocessing, copy number analysis, and customized reporting. Users can select workflows tailored for either solid or liquid biopsy analysis (e.g. circulating tumor DNA), with specific tools integrated for each sample type. The final report generated by SAMURAI provides detailed results to facilitate data interpretation and potential downstream analyses. To demonstrate its robustness, SAMURAI was validated using simulated and real-world data sets. The pipeline achieved high concordance with ground truth data and maintained consistent performance across various scenarios. By promoting standardization and offering a versatile workflow, SAMURAI empowers researchers in diverse environments to reliably analyze CNAs from sWGS data. This, in turn, holds promise for advancements in precision medicine.
(© The Author(s) 2025. Published by Oxford University Press.)

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IG 29071 Italian Association for Cancer Research; 965193 European Union's Horizon 2020; Alessandra Bono Foundation

Keywords: bioinformatics pipeline; copy number alterations; nextflow pipeline; shallow whole genome sequencing

Date Created: 20250129 Date Completed: 20250129 Latest Revision: 20250131

20250131

PMC11775468

10.1093/bib/bbaf035

39879385