ArchaeaHQ: a curated reference database of archaeal genomes

Archaea have proven to be major players in biogeochemical cycles across diverse ecosystems, yet we still see an underrepresentation of archaeal genomes in the datasets used by popular computational biology tools. Here, we present ArchaeaHQ, a quality-controlled, systematically curated reference database of 25,584 archaeal genomes compiled initially from 43,045 assemblies from all four archaeal kingdoms retrieved from NCBI: Methanobacteriati (Euryarchaeota), Thermoproteati (TACK), Nanobdellati (DPANN) and Promethearchaeati (Asgard). All genomes in the database passed standardized quality control, requiring ≥70% completeness and ≤10% contamination. A total of 44.0% of genomes in ArchaeaHQ achieved ≥90% completeness, while 92.7% exhibited ≤5% contamination. ArchaeaHQ comprises 18,701 metagenome-assembled genomes (MAGs; 73.1%) and 6,883 isolate genomes (26.9%). Approximately 76% of MAGs are assigned to 17 ecologically meaningful categories based on sampling origin, and around 65% of genomes include geographic metadata. ArchaeaHQ is available at https://doi.org/10.6084/m9.figshare.32266599 for download and at https://vee-lab.eu/archaeahq for online browsing. This resource was designed to provide an analysis-ready reference set for metagenomic, biogeochemical and ecological studies, comparative genomics analyses and the development of archaeal-specific bioinformatic tools.