Overview Update Pipeline Quality Taxonomy Environments Geography Genome Browser Compare Methods
VEE Lab Tools // Database · v2.0 · September 2026
ArchaeaHQ

ArchaeaHQ

A quality-controlled, systematically curated reference database of 25,584 archaeal genomes across all four kingdoms — filtered, de-replicated, and linked with environmental, geographic and taxonomic metadata. Built to be explored and downloaded, not just read.

Download ArchaeaHQ download Update with NCBI sync Explore the genomes Read the manuscript north_east
V2.0 Updated September 2026 · v1.0: 21,644 genomes
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Results · 01 — The Database

A High-Quality Archaeal Reference

Public archives grow fast but inconsistently — a mixture of pristine genomes, fragmented assemblies, and records with missing environmental data. ArchaeaHQ resolves that into a single analysis-ready set.

What's new in v2.0
add_circle3,940 more genomes — 25,584 genomes from a fresh retrieval of 43,045 NCBI assemblies (v1.0: 21,644 from 35,993).
account_treeTaxonomy explorer — zoom from kingdom to genus through the NCBI Taxonomy ranks of every genome.
genetics21,972 16S rRNA gene sequences recovered from 17,255 genomes, shipped as Archaea_HQ-16S.fasta.
syncUpdate it yourself — add the newest NCBI genomes with the same curation criteria using archaeahq-update — see how below.
flagNCBI contamination warnings (FCS) are now reported for every genome in Supplementary Table 1.
touch_appInteractive figures — open any environment at one dot per genome and hover sampling sites on the world map.
Abstract

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 provides an analysis-ready reference set for metagenomic classification, biogeochemical and ecological studies, comparative genomics, and development of archaeal-specific bioinformatic tools.

Full preprintRead the complete methods, results, and references on bioRxiv.
Read the manuscript north_east
How to cite

Bespiatykh, D., et al. (2026). ArchaeaHQ: A Quality-Controlled, Systematically Curated Reference Database of Archaeal Genomes. bioRxiv. https://doi.org/10.64898/2026.06.02.729493

New in v2.0 · archaeahq-update

Never Out of Date

New archaeal assemblies reach NCBI every week. With archaeahq-update you can check what has been released since your copy, run the new genomes through exactly the same curation rules, and build the next version of the database — in four commands.

Terminal
Once · install and get the database
$ pip install git+https://github.com/Pedrolleao/archaeahq-update.git
$ archaeahq-update setup      # tools + CheckM2 database
$ archaeahq-update fetch-db   # ArchaeaHQ from figshare
Every update · four commands
# 1. What is new at NCBI since my version? (nothing is downloaded)
$ archaeahq-update check

# 2. Download and evaluate the new genomes
$ archaeahq-update run --threads 24

# 3. Review the recommendations
$ less archaeahq_update_work/runs/run_*/summary.txt

# 4. Accept them: build the next database version
$ archaeahq-update release
1

See what's new check

Lists, per kingdom, the NCBI assemblies deposited after your version that have never been evaluated — including newer versions of genomes already in the database.

2

Curate the new genomes run

Downloads them and applies the ArchaeaHQ rules, stage by stage. An interrupted run resumes where it stopped.

CheckM2 · ≥70% complete, ≤10% contaminatedskani · ANI 95% species redundancy17 environment categoriesbarrnap · rRNA & tRNA
3

Review summary.txt

Every genome gets a recommendation — Add, Replace or Do not add — with the reason and the full 25-column metadata row. You stay the curator: accept all, or pass your own list with --accept.

4

Build the next version release

Writes a new versioned folder with genomes, predicted proteins, 16S rRNA sequences and the updated information table, and prints a side-by-side comparison with your previous version.

Linux or macOS with conda. The heavy tools (CheckM2, NCBI Datasets, skani, barrnap, Prodigal) are installed for you by setup. Preview any release first with release --dry-run. Step-by-step guide menu_book archaeahq-update on GitHub north_east
Results · 02 — Curation

From 43,045 Assemblies to 25,584 Genomes

A multi-step pipeline applied contamination and completeness gates, then removed identity- and species-level redundancy — a 40.6% net reduction that keeps quality high while preserving the full taxonomic spectrum.

From NCBI Assemblies to ArchaeaHQ

    Fig. 1a — Curation workflow from the 43,045 NCBI archaeal assemblies to the 25,584 ArchaeaHQ genomes. Band width is proportional to the number of assemblies; grey bands are removed at each step. Hover a band, bar, step or kingdom for its numbers.

    Unique species-level genomes retained per kingdom
    Results · 03 — Genome Quality

    Completeness & Contamination

    Every genome passed the ≥70% completeness / ≤10% contamination gate. Filled points meet the MIMAG high-quality bar (≥90% complete, ≤5% contaminated). Toggle kingdoms in the legend.

    Quality landscape

    All 25,584 genomes · CheckM2 v1.0.1 · click legend to isolate a kingdom

    Contamination (%)
    Completeness (%)

    High-quality genomes by kingdom

    Share with a Parks genome quality score above 50 (completeness − 5 × contamination)

    Results · 04 — Taxonomy

    Four Kingdoms, 39 Phyla

    Every genome keeps its NCBI taxonomy, so ArchaeaHQ plugs straight into NCBI-based tools. Open a kingdom to zoom through phylum, class, order, family and genus; at genus level the species link out to NCBI Taxonomy.

    4
    Kingdoms
    39
    Phyla
    97.4% of genomes named
    51
    Classes
    84
    Orders
    119
    Families
    307
    Genera
    24.9% of genomes named

    Taxonomic Distribution of Archaeal Genomes

      Voronoi treemap: cell area is proportional to the number of genomes. Hatched cells are genomes without a named taxon at that rank — the share of genomes with a named taxon falls from 97.4% at phylum level to 24.9% at genus level, reflecting the limited resolution of NCBI annotations for many uncultivated archaea.

      Results · 05 — Environmental Diversity

      17 Ecological Categories

      The in-depth curation of environmental context is what sets ArchaeaHQ apart. Each genome is normalized into one of 17 categories from five metadata fields. Hot springs, marine waters, soils and hydrothermal vents dominate. Click an environment to see its genomes one dot each.

      Archaeal Genome Distribution by Environment

      Parliament plot · sector = environment category, dot colour = archaeal kingdom · click an environment sector or its colour bar to open it at one dot per genome · hover a kingdom to isolate it, click to keep it

      genome assemblies

        Fig. 2 — Parliament plot of ArchaeaHQ genomes by environment category, coloured by archaeal kingdom. Percentages give each category's share of all genomes (Supplementary Tables 2–3).

        Results · 06 — Biogeography

        Global Sampling Footprint

        Geographic metadata are available for 16,617 genomes (65.0% of the database) from 2,014 distinct sampling sites, enabling spatial analyses of archaeal biogeography. Coordinates were verified from BioSample-level records during curation.

        Geographic Distribution of ArchaeaHQ Genomes

        Robinson projection · each dot is one genome, coloured by archaeal kingdom · hover a kingdom to isolate it, click to keep it · hover a site for its genomes

          Fig. 3 — Sampling locations of the 16,617 georeferenced genomes. Each dot is one genome; sites where many genomes were recovered grow a halo proportional to their number.

          Top sampling locations

          Genomes with a parseable country / ocean of origin

          Georeferenced coverage per kingdom
          The Database · Interactive

          Genome Browser

          Search and filter all 25,584 genomes by kingdom, environment, assembly type, completeness, 16S rRNA content and free text (species, accession, BioProject, country). Accessions link directly to NCBI.

          Click a column header to sort · tick rows to build a download set
          No genomes selected Tick the checkboxes to build a set, then export the accessions to fetch the sequences from NCBI.
          Results · 07 — In Context

          How ArchaeaHQ Compares

          Existing resources solve parts of the problem. ArchaeaHQ is designed specifically as a downloadable, quality-filtered, environmentally annotated archaeal reference set that stays compatible with NCBI-based workflows.

          NCBI GenBank
          Comprehensive archive
          • ✓Most comprehensive assembly archive
          • ✕Highly variable quality & completeness
          • ✕No curated archaeal subset
          • ✕Inconsistent environmental metadata
          GTDB
          Taxonomy framework · R09-RS220
          • ✓Phylogenetically consistent taxonomy
          • ~Representative genomes only
          • ✕Not an analysis-ready download set
          • ✕Diverges from NCBI accessions
          IMG/M
          JGI · rich metadata
          • ✓Large MAG collection
          • ✓Rich environmental context
          • ✕Not a precompiled download
          • ✕Hard to use in CLI pipelines
          ArchaeaHQ
          This work
          • ✓Quality-controlled & de-replicated
          • ✓Fully downloadable, analysis-ready
          • ✓Environmental data as a core feature
          • ✓NCBI taxonomy & accession compatible
          • ✓User-updatable with the same criteria
          Methods

          How It Was Built

          The reproducible pipeline behind every genome in the database.

          Use ArchaeaHQ in Your Research

          ArchaeaHQ is freely available — genomes, curated metadata and 16S rRNA sequences on figshare. Keep it current with the update script, and reach out to discuss collaborations or training in archaeal comparative genomics.

          Download ArchaeaHQ download Read the manuscript north_east Update script sync
          How to cite

          Bespiatykh, D., et al. (2026). ArchaeaHQ: A Quality-Controlled, Systematically Curated Reference Database of Archaeal Genomes. bioRxiv. https://doi.org/10.64898/2026.06.02.729493