GenArk: towards a million UCSC genome browsers

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Interactive graphical genome browsers are vital for genomics research.
• Existing browsers often lack comprehensive and up-to-date genome assemblies.
• Access to diverse and recent genome assemblies is crucial for comprehensive analysis.

Purpose of the Study:

• To create a collection of UCSC Genome Browsers for recent NCBI genome assemblies.
• To enable fast and efficient visualization of genomic annotations.
• To provide a platform for integrating diverse genomic datasets.

Main Methods:

• Developed the Genome Archive (GenArk) collection using the UCSC Genome Browser framework.
• Utilized an established track hub system for efficient data integration and visualization.
• Implemented bulk import capabilities for third-party resources, including gene models and repeat masks.

Main Results:

• Successfully integrated 3,269 NCBI genome assemblies into the GenArk collection.
• Enabled fast visualization of gene models, repeat masks, BLAT alignments, and in silico PCR results.
• Demonstrated the ability to incorporate external data, such as TOGA and Ensembl gene models.

Conclusions:

• GenArk significantly enhances access to recent genome assemblies for visualization and analysis.
• The track hub system facilitates rapid integration of diverse genomic annotations.
• This resource empowers researchers with a more complete view of genomic data.