TEN SIMPLE RULES FOR DEVELOPING BIOINFORMATICS PIPELINES FOR CLINICAL RESEARCH

Filipe Dezordi; José Bandeira do Nascimento Júnior; Giovanna Bloise de Almeida; Murilo Castro Cervato; Marcel Pinheiro Caraciolo

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Submission

Paper Title

TEN SIMPLE RULES FOR DEVELOPING BIOINFORMATICS PIPELINES FOR CLINICAL RESEARCH

Authors

Filipe Dezordi
José Bandeira do Nascimento Júnior
Giovanna Bloise de Almeida
Murilo Castro Cervato
Marcel Pinheiro Caraciolo

Modality

Poster

Subject area

Education and outreach

Publishing Date

08/11/2023

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting2023/640431-ten-simple-rules-for-developing-bioinformatics-pipelines-for-clinical-research

ISBN

978-65-272-0061-1

Keywords

pipeline, human genetics, workflow development, NGS

Summary

Next Generation Sequencing (NGS) is transforming human clinical research, and bioinformatics pipelines are mandatory to identifying clinical genetic variants. In order to build sensitive, accurate and effective pipelines, it is required careful consideration of multiple factors: from experimental design to validations. Here, we present ten simple rules for developing bioinformatics for clinical research, following best practices based on the experience of a multidisciplinary team with more than seven years of experience. Rule 1 - Invest time in the experimental design: The bioinformatics must be aligned with the wet lab. Gene panels to whole genomes require specific infrastructure from both environments. Rule 2 - Benchmark tools to select the most effective and standardized ones: There are numerous bioinformatics tools available, and when selecting components for your pipeline, it's important to consider the balance between sensitivity, accuracy, and computational resource consumption. Rule 3 - Use semantic versioning: Adopt the semantic versioning (SemVer) to registry the pipeline's changes. SemVer will help you to manage the pipeline's evolution and facilitate the error tracing. Rule 4 - Build joined with a multidisciplinary team: Developing bioinformatics pipelines for clinical research demands expertise in multiple areas, from genetics to statistics; software engineering to database management. Bringing together a diverse team will ensure that the pipeline is robust, sensitive and effective. Rule 5 - Use workflow management systems (WfMF) to facilitate the pipeline management: WfMFs such as Cromwell, Snakemake and Nextflow are popular tools adopted for bioinformatics communities owing the automatization of the computer resources management, reproducibility and scalability of the pipelines. Rule 6 - Consider cloud computing for security compliances, cost savings, scalability and elasticity: Cloud-based infrastructures combined with WfMFs provide a rapid and secure environment for large-scale genomics analysis without handling on-premise limited capabilities and access. Rule 7 - Follow best practices in code development: Python, R, and more recently Julia and Rust, are programming languages with strong bioinformatics communities. Adhering to established coding standards, quality control practices (unitary and integration tests) and SemVer will ensure that in house tools and scripts are robust, reliable and easily maintained. Rule 8 - Absence of genetic variants validation is not an option: Use gold standard samples (e.g. NA12878) and robust validation processes such as the College of American Pathologists (CAP) instrumentation program will ensure the accuracy and sensitivity of your Human DNA bioinformatics pipeline. Rule 9 - Optimize the pipeline's processes: Monitor the pipeline's performance and identify opportunities for improvement. New tools, heuristics and programming language libraries are available to optimize current processes. Rule 10 - Document the pipeline thoroughly: Effective documentation is critical for pipeline execution, reproducibility, reliability and long-term maintenance. It must include documentation of code, tools, validations and decision-making guidelines. Developing effective bioinformatics pipelines is more complex than create a simple chain of tools. By following these ten simple rules, researchers can build robust and effective pipelines that enable groundbreaking genomic discoveries in clinical research.

Title of the Event: X-Meeting / BSB 2023
City of the Event: Curitiba
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

DEZORDI, Filipe et al.. TEN SIMPLE RULES FOR DEVELOPING BIOINFORMATICS PIPELINES FOR CLINICAL RESEARCH.. In: X-Meeting presentations. Anais...Curitiba(PR) Campus da indústria, 2023. Available in: https//www.even3.com.br/anais/xmeeting2023/640431-TEN-SIMPLE-RULES-FOR-DEVELOPING-BIOINFORMATICS-PIPELINES-FOR-CLINICAL-RESEARCH. Access in: 21/06/2025