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Bpipe: a tool for running and managing bioinformatics pipelines.

Simon P Sadedin1, Bernard Pope, Alicia Oshlack

  • 1Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia. simon.sadedin@mcri.edu.au

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Summary

Bpipe is a programming language that simplifies the creation and execution of bioinformatics pipelines. It transforms shell scripts into adaptable workflows, ensuring reproducible research with controlled execution and logging.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Bioinformatics pipelines are crucial for analyzing large biological datasets.
  • Existing shell scripts can be difficult to manage, adapt, and reproduce.
  • There is a need for user-friendly tools to streamline pipeline development.

Purpose of the Study:

  • To introduce Bpipe, a novel programming language for bioinformatics pipelines.
  • To demonstrate Bpipe's ability to enhance flexibility, adaptability, and maintainability of workflows.
  • To ensure controlled, repeatable execution and reproducibility of experimental results.

Main Methods:

  • Bpipe is a dedicated programming language designed for defining and executing bioinformatics pipelines.
  • It facilitates the conversion of existing shell scripts and command-line tools into robust workflows.
  • The system requires only Java as a dependency, ensuring cross-platform compatibility.

Main Results:

  • Bpipe enables users to create highly flexible and maintainable bioinformatics workflows with minimal effort.
  • Pipelines executed with Bpipe run in a controlled and repeatable manner.
  • Comprehensive audit trails and logs are maintained for enhanced reproducibility.

Conclusions:

  • Bpipe offers a simple, self-contained, and cross-platform solution for bioinformatics pipeline management.
  • Its ease of adoption and deployment makes it ideal for diverse research environments.
  • Bpipe significantly improves the reproducibility and reliability of bioinformatics research.