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

ABSTRACT: 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.

SUBMITTER: Potente S 

PROVIDER: S-EPMC11775468 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature