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Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery.

Friederike Hanssen1,2,3,4, Maxime U Garcia5,6,7, Lasse Folkersen8

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Summary

The nf-core/sarek 3 pipeline streamlines DNA variation analysis for germline and somatic samples. This updated workflow significantly reduces storage and runtime, cutting costs by 70% for large-scale genomic data processing.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • DNA variation analysis is crucial for biomedicine, especially in comparing normal and tumor samples.
  • Large-scale sequencing efforts generate thousands of samples, necessitating scalable and automated data processing workflows.

Purpose of the Study:

  • To present nf-core/sarek 3, a rewritten, comprehensive variant calling and annotation pipeline.
  • To enhance scalability, portability, and automation for germline and somatic DNA variation analysis.

Main Methods:

  • Full rewrite of the original nf-core/sarek pipeline.
  • Implementation of the CRAM format for reduced storage requirements.
  • Increased intra-sample parallelization to decrease runtime.

Main Results:

  • Significant reduction in storage needs and processing time.
  • Achieved a 70% cost reduction in commercial cloud environments.
  • Enables large-scale, cross-platform genomic data analysis with lower costs and environmental impact.

Conclusions:

  • nf-core/sarek 3 offers a cost-effective and efficient solution for DNA variation analysis.
  • The pipeline supports any genome with a known reference, facilitating broad applicability.
  • The optimized workflow supports sustainable and large-scale genomic research.