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Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline
Yash Patel1,2,3, Chenghao Zhu1,2, Takafumi N Yamaguchi1,2,3
1Department of Human Genetics, University of California, Los Angeles, USA.
Biorxiv : the Preprint Server for Biology
|September 16, 2024
Summary
Metapipeline-DNA is a new Nextflow pipeline that automates comprehensive DNA sequencing data analysis. It processes raw reads to feature detection and visualization, enhancing genomic research scalability.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- DNA sequencing technology continues to advance in price, quality, and throughput.
- Algorithmic innovations enable the inference of diverse genomic features from sequencing data.
- Analysis of nuclear, mitochondrial, germline, and somatic genomes is increasingly sophisticated.
Purpose of the Study:
- To develop an automated and extensible meta-pipeline for comprehensive DNA sequencing data analysis.
- To streamline the process from raw sequencing reads to feature detection and visualization.
- To facilitate high-scale and integrated analysis of various genomic characteristics.
Main Methods:
- Created metapipeline-DNA, an extensible Nextflow meta-pipeline.
- Analyzes targeted and whole-genome sequencing data.
- Covers pre-processing, feature detection, quality control, and data visualization.
- Incorporates robust software engineering practices, including automated failure recovery and testing.
- Cloud-compatible and highly configurable for subsetting and optimization.
Main Results:
- Metapipeline-DNA automates the analysis of a wide range of genomic features.
- The pipeline supports both targeted and whole-genome sequencing data.
- It ensures robust analysis through automated recovery, testing, and verification.
- Facilitates comprehensive and high-scale DNA sequencing data analysis.
Conclusions:
- Metapipeline-DNA provides a unified, automated solution for complex DNA sequencing data analysis.
- Its extensible and configurable nature supports diverse research needs.
- The pipeline enhances the efficiency and scalability of genomic research.
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