GenArk: Towards a million UCSC Genome Browsers

Area of Science:

• Genomics
• Bioinformatics

Background:

• Interactive genome browsers are crucial for DNA sequence analysis.
• Managing a growing number of genome assemblies and their annotations presents significant challenges.

Approach:

• Developed the Genome Archive (GenArk) collection of UCSC Genome Browsers for NCBI-hosted assemblies.
• Utilized an established assembly hub system for on-demand visualization without database servers.
• Optimized BLAT aligner and in-silico PCR for efficient large-genome analysis with limited RAM.

Key Points:

• GenArk offers fast visualization of chromosome regions with pre-loaded annotations like gene models and repeat masks.
• Users can upload custom annotations via track hubs or import bulk data from third-party resources.
• Currently hosts 2,430 assemblies, with plans for continuous updates and community-driven additions.

Conclusions:

• GenArk significantly improves accessibility to a vast and growing number of genome assemblies.
• Facilitates comparative genomics and annotation efforts by providing a scalable visualization platform.