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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.

Cade D Mirchandani^1,2, Allison J Shultz³, Gregg W C Thomas⁴

¹Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

Molecular Biology and Evolution

|December 9, 2023

Summary

This summary is machine-generated.

A new workflow, snpArcher, standardizes genomic resequencing analysis for nonmodel organisms. This tool facilitates comparative population genomics by enabling efficient data reuse and analysis of genetic variation across species.

Keywords:

comparative population genomics conservation genomics evolutionary genomics genomic workflow

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Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Genomic resequencing data is rapidly increasing, offering opportunities for comparative population genomics.
Challenges in data reuse include variable variant calling pipelines, data quality issues, and intensive reanalysis needs.
Nonmodel organisms often lack standardized analysis pipelines for genomic data.

Purpose of the Study:

To introduce snpArcher, a flexible and efficient workflow for analyzing genomic resequencing data in nonmodel organisms.
To standardize variant calling and downstream analyses for genomic data.
To facilitate comparative population genomic studies by enabling data reuse.

Main Methods:

Developed snpArcher, a Snakemake-based workflow with modules for variant calling, quality control, visualization, and filtering.
Implemented a standardized variant calling pipeline.
Ensured compatibility with high-performance computing clusters and cloud environments.

Main Results:

Applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates.
Demonstrated the workflow's flexibility and efficiency in analyzing diverse genomic data.
Made variant data sets publicly available for future comparative analyses.

Conclusions:

snpArcher provides a user-friendly, reproducible, and efficient solution for analyzing genomic resequencing data in nonmodel organisms.
The workflow promotes the rapid use and reuse of large genomic data sets.
snpArcher will advance the understanding of genetic variation across species through enhanced comparative population genomics.