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nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis.

Charlotte West1, Charlotte Capitanchik1,2, Chris Cheshire1

  • 1The Francis Crick Institute, London, England, UK.

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|October 13, 2023
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Summary
This summary is machine-generated.

nf-core/clipseq is a robust Nextflow pipeline for analyzing crosslinking and immunoprecipitation sequencing (CLIP-seq) data. It ensures reproducible and scalable analysis, incorporating diverse tools for RNA biology research.

Keywords:
CLIPNextflowRNA-protein interactionsbioinformatic pipelinespeak callingreproducible research

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Crosslinking and immunoprecipitation (CLIP) is crucial for studying protein-RNA interactions.
  • A growing number of CLIP experimental protocols and computational tools necessitate standardized analysis pipelines.
  • Existing tools lack comprehensive documentation and integration, hindering reproducibility and scalability.

Purpose of the Study:

  • To present nf-core/clipseq, a Nextflow pipeline for robust quality control and analysis of CLIP sequencing data.
  • To provide a flexible, scalable, and reproducible bioinformatic solution for CLIP-seq data.
  • To support the molecular biology community with a gold-standard, community-curated data analysis pipeline.

Main Methods:

  • Development of a Nextflow-based computational pipeline, nf-core/clipseq.
  • Integration of multiple computational tools for CLIP-seq data analysis, including peak-calling.
  • Implementation of quality control metrics and data visualization features.
  • Adherence to nf-core community standards for workflow management, version control, and containerization.

Main Results:

  • nf-core/clipseq offers a robust, reproducible, and scalable solution for CLIP-seq data analysis.
  • The pipeline integrates diverse tools and provides quality control visualizations for informed decision-making.
  • It meets key requirements for workflow management, version control, and containerization.

Conclusions:

  • nf-core/clipseq addresses the need for a standardized, high-quality bioinformatic pipeline for CLIP-seq data.
  • The pipeline facilitates the study of protein-RNA interactions and RNA biology.
  • Continuous development and community engagement ensure the pipeline's ongoing relevance and utility.