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Related Experiment Video

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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

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BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data.

Nicholas J Eagles1, Richard Wilton2, Andrew E Jaffe1

  • 1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA.

BMC Bioinformatics
|September 13, 2023
PubMed
Summary

BiocMAP accelerates whole genome bisulfite sequencing (WGBS) analysis using GPU alignment and memory-efficient data handling. This pipeline makes complex genomic methylation profiling more accessible and computationally feasible for researchers.

Keywords:
AriocBioconductorPipelineWGBS

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • Whole genome bisulfite sequencing (WGBS) is crucial for understanding epigenetic modifications in diseases.
  • Traditional WGBS workflows face computational bottlenecks in read alignment and memory-intensive data handling.
  • Existing pipelines can be impractical for researchers due to high computational demands.

Purpose of the Study:

  • To develop a computationally efficient and memory-saving pipeline for WGBS data analysis.
  • To accelerate the alignment step using GPU-accelerated software.
  • To provide a Bioconductor-friendly workflow for broader accessibility.

Main Methods:

  • Implemented a two-module pipeline, BiocMAP, using Nextflow.
  • Module 1 utilizes Arioc, a GPU-accelerated aligner for computationally intensive read alignment.
  • Module 2 extracts and merges DNA methylation proportions in a GPU-free environment, employing on-disk data representation.

Main Results:

  • BiocMAP significantly reduces computational time for WGBS alignment.
  • The pipeline drastically lowers main memory requirements through on-disk data representation.
  • BiocMAP's output objects are compatible with R and Bioconductor, enhancing usability.

Conclusions:

  • BiocMAP offers a reproducible and efficient solution for WGBS analysis.
  • The pipeline supports various computing environments via containerization (Docker, Singularity) and schedulers (SLURM, SGE).
  • BiocMAP facilitates integration with existing open-source analytical tools for methylation data.