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Updated: Mar 20, 2026
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline
Yash Patel1, Chenghao Zhu2, Takafumi N Yamaguchi1
1Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Metapipeline-DNA automates comprehensive analysis of DNA sequencing data, from raw reads to feature detection and visualization. This open-source tool enhances genomic research by streamlining complex data processing pipelines.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Advancements in DNA sequencing technologies have led to increased data volume and complexity.
- Extracting comprehensive genomic features requires sophisticated and automated analytical approaches.
Purpose of the Study:
- To develop an extensible Nextflow metapipeline for automating the end-to-end analysis of DNA sequencing data.
- To enable comprehensive quantification of nuclear, mitochondrial, and evolutionary genomic features from germline and somatic samples.
Main Methods:
- Creation of metapipeline-DNA, a Nextflow-based metapipeline.
- Integration of preprocessing, feature detection (multiple algorithms), quality control, and data visualization.
- Implementation of robust software engineering practices: automated failure-recovery, granular testing, and parameter verification.
Main Results:
- Metapipeline-DNA successfully analyzes targeted and whole-genome sequencing data.
- The pipeline supports independent step execution, cloud compatibility, and configurable analysis options.
- Facilitates high-scale, comprehensive DNA sequencing data analysis.
Conclusions:
- Metapipeline-DNA provides a robust, automated solution for complex genomic data analysis.
- The open-source nature and modular design promote accessibility and further development in genomic research.
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