Ocean Read Atlas

Ocean Read Atlas enables rapid, high-precision indexing and querying of metagenomic sequences from the Tara Oceans dataset using kmindex to support comparative and spatial analyses.

Key Features:

• Efficient Indexing and Querying: Uses kmindex to construct sequence indexes an order of magnitude faster than previous methods and execute searches in a fraction of a second, up to two orders of magnitude faster than existing technologies.
• High Precision: Achieves false positive rates below 0.01% and represents a fourfold increase in precision over current methodologies.
• Scalability: kmindex has been used to index 1,393 marine seawater metagenome samples from the Tara Oceans project.
• Real-Time Querying: Provides real-time query capabilities on the Tara Oceans dataset.
• Geographic Visualization: Enables visualization of sequence search results on geographic maps and correlation with environmental variables collected during the Tara Oceans circumnavigation campaign.

Scientific Applications:

• Marine genomics: Facilitates metagenomic surveys by enabling rapid sequence-level searches across Tara Oceans datasets.
• Microbial diversity: Supports studies of microbial diversity through detection and comparison of sequences across samples.
• Ecosystem function: Enables investigation of ecosystem function by linking sequence presence to environmental contexts.
• Environmental associations: Supports correlation of sequence data with environmental variables to study organismal responses and adaptation across ocean regions.

Methodology:

Index construction and sequence querying are performed using kmindex; an index was built for 1,393 Tara Oceans marine seawater metagenome samples, with reported index construction speed gains of ~10× and query speed gains of ~100× versus prior methods, and measured false positive rates below 0.01%.