ArchaeaHQ: 21,644 Quality-Controlled Archaeal Genomes

ArchaeaHQ is a systematically curated reference database of 21,644 archaeal genomes compiled from NCBI assemblies. All genomes pass a standardized quality control requiring ≥70% completeness and ≤10% contamination, with 44.2% achieving ≥90% completeness. The database was created by Pedro Leão and last updated in May 2026.

Use Cases

• Metagenomic classification using a quality-controlled reference set of archaeal genomes.
• Biogeochemical and ecological studies based on genomes categorized by sampling origin.
• Comparative genomics leveraging genomes from all four archaeal kingdoms.
• Development of archaeal-specific bioinformatic tools using a standardized genome database.

Strengths

• Contains 21,644 archaeal genomes from four kingdoms, sourced from 35,993 initial assemblies.
• All genomes meet strict quality thresholds: ≥70% completeness and ≤10% contamination.
• Includes 16,199 metagenome-assembled genomes (MAGs) and 5,445 isolate genomes.
• 74.8% of MAGs are classified into 17 ecologically meaningful categories based on sampling origin.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect geographic or source bias inherent to the original NCBI assemblies.

Provenance

Source

NCBI assemblies.

Collection Method

Compiled and curated from retrieved assemblies, with standardized quality control applied.

Freshness

Last updated 2026-05-22 13:07:36; freshness should be verified.

Geography

65.4% of genomes present geographic metadata, but specific coverage is not detailed.