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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Experiences with workflows for automating data-intensive bioinformatics.

Ola Spjuth1, Erik Bongcam-Rudloff2, Guillermo Carrasco Hernández3

  • 1Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, P.O. Box 591, Sweden. ola.spjuth@farmbio.uu.se.

Biology Direct
|August 19, 2015
PubMed
Summary
This summary is machine-generated.

Bioinformatics pipelines benefit from workflow systems for reproducibility and automation. However, current systems have overhead, leading to fragmented solutions. Recommendations are provided for simpler, efficient workflow construction.

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Area of Science:

  • Bioinformatics and Computational Biology
  • Genomics and Molecular Biology

Background:

  • High-throughput technologies like next-generation sequencing have made molecular biology data-intensive.
  • Bioinformaticians require high-performance computing for large-scale data management and analysis.
  • Workflow systems can automate tasks, enhance reproducibility, and provide fault tolerance in analysis pipelines.

Purpose of the Study:

  • To analyze the experiences with workflow systems in the bioinformatics community through EU COST action SeqAhead hackathons and workshops.
  • To identify inefficiencies and fragmentation caused by diverse solutions to similar bioinformatics problems.
  • To develop recommendations for future systems that simplify bioinformatics workflow construction and execution.

Main Methods:

  • Community engagement through hackathons and workshops.
  • Analysis of diverse strategies and solutions employed by participating organizations.
  • Synthesis of experiences to identify common challenges and best practices.

Main Results:

  • Significant fragmentation of efforts and development of redundant, incompatible solutions across organizations.
  • Workflow systems, while beneficial, often involve substantial development and administration overhead.
  • A shared need for more efficient and user-friendly bioinformatics workflow construction tools was identified.

Conclusions:

  • The current fragmentation of bioinformatics workflow development is inefficient.
  • Future workflow systems should prioritize ease of use and efficient construction.
  • Recommendations are proposed to foster more unified and effective bioinformatics pipeline development.