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

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Published on: April 4, 2018

Refgenie: a reference genome resource manager.

Michał Stolarczyk¹, Vincent P Reuter¹, Jason P Smith^1,2

¹Center for Public Health Genomics, University of Virginia, PO Box 800717, Charlottesville, VA, 22908, USA.

|January 30, 2020

Summary

This summary is machine-generated.

Managing reference genome assemblies and their associated data is crucial for genomics research. Refgenie is a new tool that simplifies organizing, retrieving, and sharing these essential genome analysis resources.

Keywords:

data management data portability reference assemblies reference genomes

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Reference genome assemblies are fundamental for high-throughput sequencing analyses.
Genome assemblies and related resources, such as indexes, are typically stored locally.
Sharing these essential resources is currently challenging due to a lack of simple tools.

Purpose of the Study:

Introduce refgenie, a novel reference genome assembly asset manager.
Facilitate the organization, retrieval, and sharing of genome analysis resources.
Provide a versatile tool for both computational tool development and data analysis.

Main Methods:

Developed refgenie as a command-line interface (CLI) tool.
Implemented a server application with a RESTful API for broader accessibility.
Designed refgenie to manage various reference genome-related files, including sequences and indexes.

Main Results:

Refgenie simplifies the management of genome analysis resources.
The tool supports the organization and sharing of genome indexes, sequences, and annotation files.
Both CLI and API provide flexible access for diverse user needs.

Conclusions:

Refgenie streamlines the sharing of genome analysis resources across research groups and computing environments.
The tool enhances collaboration and reproducibility in genomics research.
Refgenie is readily available at https://refgenie.databio.org.