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Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers.
Wratten, Laura; Wilm, Andreas; Göke, Jonathan.
Afiliação
  • Wratten L; Genome Institute of Singapore, Singapore, Singapore.
  • Wilm A; ImmunoScape, Singapore, Singapore.
  • Göke J; Genome Institute of Singapore, Singapore, Singapore. gokej@gis.a-star.edu.sg.
Nat Methods ; 18(10): 1161-1168, 2021 10.
Article em En | MEDLINE | ID: mdl-34556866
The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not just for experiments, but also for computational analysis. However, transforming data into information involves running a large number of tools, optimizing parameters, and integrating dynamically changing reference data. Workflow managers were developed in response to such challenges. They simplify pipeline development, optimize resource usage, handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing. In this Perspective, we highlight key features of workflow managers, compare commonly used approaches for bioinformatics workflows, and provide a guide for computational and noncomputational users. We outline community-curated pipeline initiatives that enable novice and experienced users to perform complex, best-practice analyses without having to manually assemble workflows. In sum, we illustrate how workflow managers contribute to making computational analysis in biomedical research shareable, scalable, and reproducible.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Biologia Computacional / Pesquisa Biomédica / Fluxo de Trabalho Tipo de estudo: Guideline / Prognostic_studies Idioma: En Revista: Nat Methods Assunto da revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Singapura

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Biologia Computacional / Pesquisa Biomédica / Fluxo de Trabalho Tipo de estudo: Guideline / Prognostic_studies Idioma: En Revista: Nat Methods Assunto da revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Singapura